There's some evidence saying GJ can effect the soul but that'll derail the thread. GJ dosen't ALWAYS manipulate chakra flow there was actually a thread on that about a month ago. Sharingan users have feats of mind haxing tailed beast when they don't have a physical form
So this guy instantly develops resistance and his phone activates automatically if something bad happens to him? Also how exactly does his pocket world work because jinchurki have a inner mental plane where their biju are and Sharingan users can go in there to interact with them
But besides limbo and Genjutsu madara also has truth seeking orbs power mimicry can comeback to life atleast once sealing absorption clones etc.
Don't tailed beast are made from chakra? Because in that case I don't know if it count since it's still the same type of energy. And if the genjutsu isn't sure that affect the soul then probably isn't gonna work against him.
Basically, at the beginning of series for example developed pretty quickly resistance to biological manip and also developed several abilities, with the illusory world he faced he did go from not having resistance to illusion manip to resist it despite be layered, the first time he faced a a layered and pretty potent soul manip thing (which basically was like a soul crush with the different effects and all) he developed a resistance in moments and also developed three more abilities, and probably more examples that I'm forgeting. As a side note his stats also grow pretty fast, with statements that he grow each second and feats like stomp a perfect copy of the him from seconds ago. His companions (the girls from the main group) are comparable to him regarding their adaptation/development of resistances and powers and grow in stats.
And yes, the smartphone is constantly monitoring his state and the moment an abnormality is detected they it automatically activate a time manip artifact to revert the damaged or effects that affected him. In one point the OP said that the resurrection qork as long there is something left but actually that's incorrect, is a missunderstanding about comments saying in the main story (when the still didn't developed much the time manip magic and didn't had infinite magic power), that there is something left just help in the sense that not consume as much magic power (same with the time limit they had) but by the after stories they show to be able to ressurect someone even without anything left and with their current infinite magic power the consumption isn't a problem anymore. The smartphone is in his pocket world, the girls also have a smartphone.
The pocket world is in his ring, originally it was only a dimensional storage via spatial manip but current he have developed much more the thing, basically recreating the cosmology of the verse inside though in a minor scale (that's why is called Miniature Garden), the current size of the world is unknow but at the very least is know that the first two weeks in their expantion there already existed two continents and the after story have advanced 4 years after that. Inside the Miniature Garden habit several incorporeal demos withou physical body that have the following haxs do to have magic of the age of gods (spatial, gravity, time, matter, biological, soul, mind and info manip, maybe also something more that I forgot), abstracts existences like dragons with also a great variety of haxs (included layered death hax since it's possible/probably that Yato no Kami or other apparitions with similar powers migrated inside), robots/Ais, all the artifacts of Hajime and possibly more devending of how much he developed the Miniature Garden, ah, and also all the energy inside the Miniature Garden is controled by elementals (which possibly are also abstracts, this need to be discussed more in the general thread) who follow Hajime orders.
Don't know how the orbs would interact with Hajime artifacts since they have most of the haxs.
Does Hajime start with speed amp because i don't think he can resist this scaling chain
Basically yes, the only times when he don't actually begin with that is when playing around facing complete fodder to him. Also, the 12x amp is the basic amp, he can futher amp that with and 3x and 5x amp if wanted (this are amps in general to all his stats), on top of a buff via info manip.