Hey there , I just joined today but I think I can help with some of these questions (I've been rewatching the various Yu-Gi-Oh series so much of this information is fresh in my mind).
I won't comment on the Duel Terminal stuff as I'm not familiar with the source material , as for the rest:
Yubel/Super Fusion/12 Dimensions: Super Fusion needs a specific process involving the sacrifice of several people in order to create and the sacrifice of even more people in order to complete (the two steps are carried out by Bronn and the Supreme King respectively) , however , once the card is completed , it persists in it's complete form and can be used as is , no further prep is required (summoning the Super Fusion God to merge the 12 Dimensions does require fusing 12 monsters ranging from level 1 to 12 , a feat which can't be accomplished without the Chain Material card due to how duels work).
Yubel never had the Super Fusion in her deck , she stole it from Judai during their duel (who had it because he completed the card as the Supreme King after taking it from Bronn). She can only be argued to "have ownership of it" after she fuses with Judai (because it's in Judai's deck). Perhaps a separate profile should be made for Super Fusion/The Super Fusion God instead ?
The 12 Dimensions are universe sized each (Misawa explains that they're parallel worlds to the main human universe that operate according to quantum theory , when describing the 12 Dimensions their representations are shown as being of the same size as that of the regular universe and lastly , the regular human universe is just one of the 12 Dimensions).
The Sacred Beasts (which Yubel scales to) might not have any power comparisons with the Egyptian Gods but Exodia (whose power Yubel also overcomes) scales to Zorc (who causes a solar eclipse among other things).
Yusei Fudo and Jack Atlas: they do have access to some fairly potent abilities (Clear Mind and it's variants for Yusei and Burning Soul for Jack) , Yusei's Over Top Clear Mind is explicitly superior to Antinomy's Top Clear Mind (it also allows him to survive in space in his duel with Z-ONE) which caused a nearby star to collapse into a black hole , an actual star/black hole as indicated by Antinomy and Yusei's-both geniuses in quantum mechanics and physics in general- use of real life elements such as core accretion and the inability of even light to escape and (with some help from Antinomy giving him a boost) , he does accelerate enough to escape the pull of the black hole (heck , the episode's title is "faster than light") and Jack's Burning Soul , much like that of the original Legendary Signer , overwhelms the power of Scar Red Nova (who gave the Crimson Dragon a tough fight , the Crimson Dragon being an actual star-the Dragon Star-visible in the night sky among other things). That said , the potency of the aforementioned abilities should not be misconstrued as something that translates to permanent physical stats. The Clear Mind variants can only be used in a Riding Duel (it should also be noted that while Yusei and Antinomy survive being in proximity to the star they are on an Yliaster-made ring of light circling it and built to serve as a course , it's likely that they were shielded from the main brunt of the damage) and Burning Soul is a termporary "super mode" that manifests when the Crimson Dragon channels it's power through the Signer who posesses the ability.
When their abilities are not active , Yusei and Jack are still superhuman (there's a lot of moderately superhuman physical stuff across the installments) but nowhere near as powerful as when the abilities are active.
Kaiba: Correct , same for Marik and all other Egyptian God wielders barring Atem , the modern wielders can't even make use of all the powers of their Millenium Items much less their gods. Kaiba's summons could only contend with Zorc in the anime because of the special conditions of the millenium world.
Don Thousand/The Astral Barian Worlds/ZEXAl profiles in general: The Astral World and Barian World are likely (though not certainly) universe sized , they are consistently described as paralled dimensions to the regular universe and , far more importantly, during the final duel between Nasch/Ryoga and Yuma , Nasch uses Don Thousand's power (which has been passed to him after the latter's death) to bring the Astral World , Barian World and Human World together and eventually cause them to collide. In this duel/these episodes the three worlds are represented as three swirling masses of energy visually similar to a spiral galaxy (red for Barian , blue for Astral , yellow for Human) and all three masses are of almost equal size (the human one is a bit smaller than the others actually). The human world depicted there is clearly not the planet Earth , it's (due to being depicted the same way as how the other dimensions are) most likely the dimension within which the Earth is contained itself.
Don Thousand pulls Earth into the Barian World using the Fusioniser , yes , but the power of the Fusioniser came from the fake Number cards which Don Thousand created using his power (or more accurately the power of Number 96 Dark Mist who had acquired the power of Chaos through the Barian Force card Vector gave him) ,he did send them to Earth to brainwash those who came to hold them and turn them into energy to make the merge progress to be sure but the merge started before that and the process was very swift besides , it takes place over the course of a day at most.
Speaking of Dark Mist (or to be more accurate it's Chaos evolved version Dark Storm) , it's rampage was inflicting heavy damage on all three worlds and was eventually going to destroy them outright (as confirmed by Astral , the Barian Emperors and Dark Mist/Storm itself) and Dark Storm is simply a fragment of Don Thousand's power that was knocked loose during his fight with Astral and entered Astral's body and was further powered up by the power of Chaos (which Don Thousand is the strongest user of anyway).
Astral's final Shining Draw in his original fight with Don Thousand almost destroyed the Astral World (we see almost the entirety of it's substance scattering explosively in all directions) , both combatants survived (though they were heavily injured and in DT's case sealed away).
The original ZEXAL morph has the power to block a blast that was going to destroy Astral World while using the Ultimate Shield ZEXAL Weapon (said blast is made up of the energy of the 50 members of the original numbers that make up Astral's memories) , Number 92:Heart-eartH posesses the combined power of the aforementioned 50 numbers ,and it's chaos form Heart-eartH Dragon can manipulate the aforementioned blast (grab it with it's mouth , fire it etc) , Tron and Kazuma Tsukumo working together can prevent the three worlds from smashing into each other during the Nasch-Yuma duel and much more.
In short most ZEXAL profiles need need a few updates.
Numeron Dragon/Numeron Code: The former created all of reality in Zexal (this includes the Astral World , the Barian World , Sargasso which is to say the void between dimensions , the in-between dimension where Yuma and Alit had their final duel (it has stars and everything) and the dimensional void Yuma found himself in when trying to reach the Astral World to get back Astral (possibly more , the Astral World only seems to be one of many dimensions the void leads to but the lack of explanation makes it impossible to tell for sure.
The Numeron Code is a fragment of the Numeron Dragon's power and contains it's feelings and knowledge , it is consistently described as capable of deciding the fate of all reality not just in the present but in the past as well (rewriting it's very history) and contains the records of all things that exist (the Akashic Records in the form of a card basically). Astral is it's wielder as of the end of the series.
Zarc: Not much to add here. Zarc's duel with Ray split the Original Dimension into the 4 Dimensions seen in Arc-V (in episode 139 Leo states that the split was something Zarc did due to being in pain as he was being split into 4 , this is further supported by how each dimension is altered based on the nature of Zarc's dragons , with the Standard Dimension becoming the Pendulum Dimension after the second split to mirror Odd-Eye's own alteration from Normal to Pendulum). The four En cards Ray uses can overcome Zarc's power and split him and the first dimensional split had the 4 dimensions come into being with an already made history (Leo was watching the Zarc-Ray duel and suddenly found himself in a park in Standard where children were dueling.
Why is Zarc listed as a "power-up" of Yuya though ? They are different people , Yuya was just a vessel (same for the other Yus) and his soul is not Zarc's soul (it's in Reira right now whereas Yuya is still in his body).
There's much more to list (Arc-V Solid Vision monsters building level ? What about Chaos Giants ? Dark Side Of Dimensions stuff , Light Of Destruction , Gentle Darkness , Darkness/Nightshroud and so on) , I'll try to get to it when I can though I might need some help (not sure how I should provide evidence from the episodes other than giving episode numbers and time stamps).