Unfortunately, moving the icons will require properly removing existing icons, and while I can certainly do that in the OCP install script, that leaves people doing stuff manually in the lurch, because that's one more step to add to avoid having duplicate images, one of which won't actually do anything anymore
.
TL;DR: That's probably not going to happen. If it seriously tickles someone's OCD, fixing it manually is trivial, as mentioned earlier.
But as a general default, it's a bit too late for that, unfortunately. And I'm wary of making the install script be a special snowflake in how it lays stuff out.
(It never personally bothered me, because I have nothing in the root folder short of, well, folders, so I didn't really think about it, but, yeah, in hindsight, I should have moved everything in a folder way back when).