This is a known issue. (Devs are aware of it.) From what I gather, they can't really fix it in a way that won't break some saves. (I can think of a few ways, but they're all complex and horrible.)
The only workaround for it is to basically exhaust everything before pushing on with the main story. Even then, you'll get some overlap if you progress in certain ways. My advice would be to advance the newest house member until they block, before picking up news ones, or moving on with the story. It's a hacky solution to a problem that stems from the game being years old and their assumption being that people will play it (unguided) as if it were being released to them.
The good news is that newer content gets better at it.
The bad news is that there are a host of 'legacy' triggers that you could trip over later.
To throw in my two cents, I don't mind the 'filler' that much. I don't like the Lost and Found filler much, because it feels like those are all dead ends, but it's possible that all of that is part of lore building (to stop a plot hole later). But with that said, we get story progression every update. The issue is that people want specific stories advanced, and there's the main story, the 'find out about the main character' masked subplot/story, and every girl has their own primary story, as well as their own sex storyline.
We've stopped getting so much of the sex storyline stuff (I'm more than fine with that), and it has been replaced by generic filler (so it feels more scattershot). But the filler/sex content didn't really block the real story progression being released. So the issue is now that for one story to advance, others have to be at a point where it doesn't add to the existing story progression issues.
Rae's story releases had to come together (if you consider update sizes, it being split made sense). The problem with that release block is that a lot of people didn't care for/about the art (I'm 'didn't care about'), so it felt light on the written/spoken content in exchange for something that I could take a pass on. (I played a lot of VNs and AVNs back when animations were rare, or not even there, so I'd have been fine with more talking.) The other problem is that I feel the devs are taking a lot of feedback on story arcs, so the story is probably in flux. Though Rae's reveal was kind of a shrug for me, because most of it was obvious, and none of it changes how I read her character. (The only 'lie' was that we didn't save her when we pulled her into the house; she reverts her position on that. It may not have been a lie, she may only have pieced it together afterwards, and the way she originally phrased it may have been more a sign that she thought that she could handle herself.)
If we take the story progression and compare it to other games, we're getting a similar amount of content to other games with similar sized teams (when factoring time). The problem is, as before, the percentage of filler content to main content masks that, as, in other, more linear, games, the way it's slipstreamed in impacts it. On the whole, I shrug.
