Time for opening arguments lets go
Due to Marx's Similarly to Vacteria's fight with Prime Tomato, I don't see too many abilities that would become strong issues. Explosion manipulation won't be a problem due to Prime Tomato directly tanking incredibly large explosions far stronger than those of the boss mines (at least from their description). Summons can be mostly negated by clones. The fear manipulation sounds much more like social influencing (instigating fear in specific), lacking enough scans to seriously be considered that ability. Prime Tomato has an incredibly heavy LS advantage, so Graviton Palms shouldn't be the largest issue.
The only one that looks to be the largest potential issue is the electricity manipulation, which Prime Tomato lacks a direct resistance to. However, there seems to be something that Prime Tomato has to negate most of this issue: I researched a little bit about the applications of lightning, and it looks like Prime Tomato won't be super affected by it...real life lightning causes mainly burns (heat, that of which prime tomato has a heavy resistance to), and electrocution
only if there's a conductor (something like metal or an equivalent). For death by electric chair, a human has to have some conductors placed on them for the electricity to work for similar reasons. Prime Tomato doesn't have any conductors attached to him, so given the effects of IRL lightning and the attack description (that it destroys surrounding ground) it'll act much more like an incredibly hot AP attack - one that Prime Tomato can tank due to his far higher AP and his incredible heat resistance.
On that note, Prime Tomato has plenty of stuff that can hurt Marx. If the 5.28x AP advantage wasn't enough, Prime Tomato's heat is enough to vaporize him, which is one-shot potential and enough to negate his Mid regeneration due to turning the dude to ash. He does have information analysis, but it's limited to getting an opponent's disaster level. Looking at the One-Punch Man page on VSBW and characters who scale relatively to Prime Tomato's AP, this should put him at the level of a Class S hero or a Dragon Level threat. IDK what this means exactly but yeah :3
Regardless, Marx is likely going to push Prime Tomato into his 3rd form really quickly given his danmaku and noticeable abilities. Marx is going to have to deal with Prime Tomato's fear aura (that of which he lacks a resistance to and may make his moves sloppier), blitz-level speed amps, clones and telekinesis (that of which seems to be one of the few abilities that can bypass his shields, something that previous characters have struggled with). While not super noticeable, his regeneration and Marx's lack of AP/abilities to hurt him will be enough to allow Prime Tomato to not take any sustained damage.
This is a close match for sure, but Prime Tomato does have the edge >:3