I had to look that up, never seen that term Diabolus Ex Machina before. Cool didn't know that had a term like that I'mma steal it lol.
The only reason I don't really have an issue when I read that was cause it didn't matter. The MC and/or FMC would win the battle using said deus ex machina and really it could have transformed into a giant puppy that was a fluff boi and I'd have still been uniterested in the enemy thing. For the record I think it's dumb that something that dies can evolve and yes it's incredibly dumb that not only does MC not tell FMC about this kind of thing earlier but apparently it was semi-common knowledge that it did.
Reason he didn't tell her was because it was not supposed to happen, we literally have an entire chapter dedicated to reasoning what just happened, why it must have happened and how it was supposedly impossible; someone or something had manipulated things from behind in order to make the creature evolve, and our MC got caught in the scheme, transforming his easy boss raid into a battle for survival.
As for things evolving after dying, well, I can kinda share the sentiment, but we gotta remember they are in a game world with game world rules (hence all the skill leveling shenanigans), and if Dark Souls has taught us anything, is that absolutely NOTHING is truly dead until it drops the loot.