I think this is fully intended. When Rem put out the first public alpha, with only a single floor of the prison, it was supposed to be a demo of everything that the game would eventually end up being... which meant that the degree of corruption you would expect to see over the course of the full story had to happen, in a compressed and accelerated format, within a single level. Later updates added more story and more than tripled the amount of space you had to play with, but they were all built upon the foundation of that first demo, which had things going waay too fast, so they had to escalate from there, leading to things like the floor 3 boss being invincible unless you farmed NG+ or had one of a small set of perfect builds. Now that they've got a decent patron base and lots of eyes on the project, and are approaching something that could be called a finished product in a few more months, they're trying to get it closer to what the end result is supposed to be.
IIRC Rem has said the "intended" experience is eventually supposed to be a Prisoner run where you genuinely try to stay pure, gradually become corrupt, but never fall to the point where you can't keep progressing the story and eventually get to an ending. Which is a significant change from previous version where Prisoner mode took a specialized build or NG+ bonuses just to make it to the halfway point. Obviously we've got a lot of balance and rebalance patches between here and v1.0, but it's probably a lot closer.
