Well, learning a new directory structure takes barely any time (people coming from Windows complain about that and I don't get the problem in that case either, like, it's something new, just learn it, it's cool to learn things and it may be better than what you're used to, and in their case it definitely is).

There are even single images out there that explain the basics of the Linux structure. Those are nice. A single condensed resource that gives people the general idea of it. Getting used to it takes some more, but that's about it, and really, most of the time you are in your home directory, so if that works somewhat similarly, it's fine.

Anyway, I think I would maybe prefer if each program had its own directory (though it could complicate adding things to PATH, I guess). But not the Windows way, Windows install programs programs in specific directories, but just scatters files everywhere, in hidden directories. Unix, on the other hand, scatters files belonging to each program everywhere, and that is also a gigantic mess, so, I don't think that is optimal at all, and some distributions have actually changed it to solve problems.

There are distributions that changed this, like Gobo (it places each program in its own directory, and apparently it can handle multiple versions of each program, just by changing the directory tree). I remember seeing one more two other distributions that did this, I think one is Sabotage, and I forgot the other one (I thought it was maybe Carbs, but apparently not), but Gobo is the biggest one, and it's already not very big. Sabotage is really small and also looks dead.

Also, package managers like Guix and Nix do their own thing as well, but last time I checked, the directory names looked like absolute hell. They may also allow multiple versions of programs and dependencies, and older version. I mean, that's half of the point of them even exist, as far as I'm aware.

Anyway, you could also go with a hybrid approach, and have a different directory structure, but also link the most recent versions of everything to where they are expected to be on a Unix system, and then you keep the compatibility with everything else. I think Gobo does this? Not sure if the others do.

In case you're interested:
https://gobolinux.org/

Also, here is Carbs:
https://carbslinux.org/
It's actually irrelevant, but it's one of the few source-based distributions out there other than Gentoo. One than that it's just Crux, and I think KISS, and maybe Venom if that's still around. Source Mage was still dead last time I checked. Have you ever used Source Mage, by the way? And what do you think about it? Actually kinda curious about it, because you were already using Linux when it was still alive.

Anyway, as far as commands go, yeah, you may have to learn new ones, and hopefully they exist. Though Haiku does have bash, so maybe they also have their own versions of tools like that. I'm pretty sure that you can install packages through the command line, so, they actually do give a shit about it, it's not GUI-only.