@DLRevan Thanks for the respectful response, I understand what you mean now. I guess the gist of it is how the manga "presents" all of these different things, and due to that presentation, expectations and standards are made, or changed. If anything, I believe the issue many people have stems from the fact that the presentation of Chapters 1-11 is vastly different to Chapter 12 and the now infamous Chapters 13-14. Yes, there have been many "degenerate" things in earlier chapters, but they were presented in a vastly more lighthearted or comedic manner.
In contrast, Chapter 12, and to an even more drastic extent, Chapters 13-14, are presented completely differently. The body horror rape thing from Chapter 12 was played a bit for laughs at the end with it just being a dream sequence, but even then it was still pretty uncomfortable and to be honest I didn't like that chapter anyway much like how I don't like the last two. As for Chapters 13 and 14, the presentation was even far more drastically changed. The lighthearted comedic aspect is practically gone, hence the claims of a "tone change" by fans, and for two whole chapters we have this very significant uncomfortable feeling as the MC goes evil and rapes half the main cast through blackmail and manipulation. It isn't portrayed as this "haha funni" thing which the rest of the series has done. It instead feels like something out of Redo of Healer.
Perhaps if the story was presented differently by the author, fans would've been fine with it, but right now it just appears to many as a formerly lighthearted comedy manga switching to a weirdly serious situation. The series has very clearly been satire from the start, yes, but satire/parody is still subject to differences of presentation, and the satire of this manga has always been presented in a pretty lighthearted manner. But the recent developments in Chapters 13-14 have instead been presented as this dramatic plot twist where things have gone bad, just look at evil MC's facial expressions on some pages. They focus on that and portray it as some dramatic negative event, where's the satirical jokes?
How will the author possibly conclude this arc in a way which suits the "overall tone" of the series you speak of? I can't see how it'll just end with the MC and the girls having a laugh like always. You say that it's fine as long as the author can "use that trope and turn it around for comedic (and presumably impermanent) purpose", but the issue for many people is, how can he possibly do that? The story tropes of NTR (or pseudo NTR in this case) and rape are being presented as a significant story issue here, with some characters being raped against their will and a potential war, it's not some inconsequential filler arc which can just be joked about at the end. Some characters are freaking out about evil MC like he's the main antagonist now. It's gone full serious.
To be honest, my thoughts on this arc will depend on how it ends. If the author manages to do a 200IQ play and somehow conclude it in a way which suits the "overall satirical parody tone", then it might be acceptable, but so far the presentation of the arc has been pretty drastically different from the rest of the story, something which has alienated many readers as seen in the rest of the comments.
At least, that's my take on it. Readers will always have standards so it shouldn't be surprising when they react based on those standards.