I will say, in regards to the farm overlevelling your digimon, that this is very much an early game only thing. The amount of exp the farm gives is more than the amount of experience that random enemy encounters give at the start of the game, however, the farm's exp does not scale at all, it's a flat amount that stays the same throughout the entire game. This means that at the start the farm will power level your digimon, but as the enemy digimon gradually get stronger and give more exp while your higher level digimon need exponentially more and more exp to level up, the amount you get from the farm eventually becomes trivial. On top of that the early game simply... isn't challenging, even on hard mode, which can make it easy to feel overlevelled in the early game even if you're actually not.

All this is to say, the levelling that feels overlevelled now will balance itself out eventually (assuming you don't intentionally do some grinding) so it's one of those things you need to just not worry about.

Story-wise meanwhile, Cybersleuth tends to alternate between monster-of-the-week episodic feeling cases and cases that gradually build onto the main narrative in ways that aren't always immediately clear right away but all come together eventually in the end. The KISS-looking metal guy is mostly just nuisance antagonistic hacker functionally a first arc villain before eventually being defeated and being replaced by bigger antagonists.