The directory and file distribution isn't really a mess, it's just something your not used to since it's basically a entirely different style if your used to windows, 6 months ago i'd have agreed with you though, but honestly if your using a more user friendly distro like garuda, it's pretty easy to figure out 95%+ of things location, especially if your using the proper app helper's.
As for prefixes, i'm honestly not sure what your complaint is, the "prefix" is basically where everything windows is to make a windows environment, for me i made a folder in my home folder called "games", that's my prefix for everything windows including games that i install manually, usually through lutris as it makes it simpler to let lutris handle it (lutris is designed for games but you can use it for programs as well if you want) so in my games folder is basically a drive c folder, which is basically a windows file structure, with the save paths the same as windows, games where i put them, programs where i put them, etc, anything i need from windows, the only thing that is not stored directly in the folder is wine itself.
A example of what i mean, let's use a wine used "yar har" version of i donno, fallout 3 or something like that as a example, the save location will be in the windows folder structure of your designed prefix, making it pretty simple to locate.
For steam it's even easier as you can just look up it's location on the pcgamingwiki as most of those have a linux version save location.
As for applimage, i've honestly never ran into this problem with applimage but i might be a exception.
