Personally, I don't see why one should be discouraged by that. I mean, even if something is made by Japanese nerds for other Japanese nerds, I don't think that's any reason for why someone out of that audience wouldn't find something they enjoy from that.
Like you said, there's always the possibility of things having a deeper meaning, and whether someone finds that deeper meaning on something that seems to be made solely to "pander to otakus", well that's entirely up to people. Everyone can have their own perspective on things they like and things they don't, and whether someone else finds that agreeable or not it doesn't really have to take away validity from your own opinion. I mean, another apparently unpopular opinion from me (or maybe it's not, really don't know how to gauge these things), I like the Byleth/Rhea pair and think it's one of the best endings in Three Houses. That doesn't change the fact that some people find it rather distasteful or think it's just a kink, and well, I can't really go around telling people what to think, I just don't agree with that and have my reasons for liking the pairing (and while I personally think it's one of the best endings, I won't say it should be that for everyone else), but if someone wants to think like that, they're welcome to it.
My point is, there's many opinions out there, but something being made "for otakus" by other Japanese nerds doesn't mean someone who isn't that can't find some deeper meaning in said tropes, or that it's wrong to like them even if they don't find anything of the sort. I mean, I don't really ship Corrin/Camilla, but I won't say that it's wrong for someone else to ship them either. Yeah, their interactions were clearly meant to invoke the "mommy kink" trope, but I mean, someone else who does like that pair could also be seeing something that I (or other people) are missing, and that's pretty cool really (at least, I think it is).