I really want to rant right now, but I'll just leave this as a cautionary tale because there might be some person who'll end up in the same spot as me one day.
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I know that obtuse mechanics that don't get fully explained until it fucks you in the ass out of nowhere and you realize you've been doing things wrong the entire time is part of the whole masochistic and autistic Venus Blood experience, but still.
tl;dr these things actually affect the Ether Core (the game over if this room explodes room). And on higher difficulties and later chapters, they hit like a motherfucker for the rooms.
In the spots early game, you can probably safely ignore these things. But for this particular case, it was a NG+ late game Law route and I was playing on hard difficulty. The whole time I thought that these only affected regular rooms, so I just figured that I'll just rebuild the rooms that get destroyed. Enemies are really aggressive and tanky on higher difficulties, so you'll have your hands full just intercepting them. But then I noticed that after a few turns, I got a random game over. I thought that I reached the turn limit, but no dice, I still had many turns to spare. I reloaded a couple of older saves thinking I got a corrupted save, but upon reaching the same point, instant game over out of nowhere. I even redownloaded the entire game thinking I might've gotten a corrupt and screwy download, but still the same results.
Two hours of trial and error and frustration later, I noticed the the Ether core had a sliver of health left, this is despite no enemy having reached the Ether core room yet. And then it all clicked. All this pain in the ass could've been avoided if the game had a simple "Ether core was destroyed!" prompt when it does. Instead, it just abruptly cuts to a game over screen with no explanation.
So if you're wondering why the game randomly shoves a game over screen to your face, then you're probably oblivious to the fact that the enemy is shelling your Ether cores without you knowing.