I think the plot became sloppy because the author try to make it up after the rxpe plot. I heard the author got criticized a lot because of that rxpe plot and went into hiatus. So I guess that's why the plot is sloppy and out of place. I bet the author try to make a new plot so the readers would not get mad again.
Yeah, i fully think the rape subplot was setup for a "who's the daddy" arc but the readers (me included) got their pitchforks out. It's just the author wrote such a cool omega (up to that point) and then wrote an unnecessary rape. Like i would be fine if author wrote a genuine love triangle with consensual sex but alas. Now this season feels like it's abruptly walking back the season 1 ending.

genuinely the plot feels like slop, at first it was good but then the unnecessary rape, it could've been avoided??? and like im so disappointed that theres no groveling arc and the chasing arc was so short, what is this shit bruh