Looking around my own cluttered home folder, the pattern seems to be that applications will split their "singlefolder" into a subtree.
For example:
- .sdkman has: bin, candidates, contrib, etc, ext, libexec, src, tmp, var
- .gitkraken has: logs, notif, profiles, repohooks, service, themes
- .mullvad-browser has: Downloads, .cache, .config, .local, .mullvad
- .dropbox has: events, instance1, instance_db, logs, machine_storage, metrics, ssa_events
- .steam has: bin, bin32, bin64, debian-installation, root, sdk32, sdk64, steam
- .xpipe has: cache, logs, settings, shell, storage, webview
...etc
I will say that even though I really don't like having a cluttered home folder, I do appreciate things being more or less in one place and so can be easily uninstalled and cleaned up. Flatsweep even being a thing is a testament to the tedium created by dispersing everything across the file system. It reminds me of macOS and not in a good way: I had an equivalent to Flatsweep on my old macbook but I couldn't remember its name so I searched "macos app cleanup tool", and the first page is just a bunch of comparison articles for the 10 (or whatever) best cleanup tools. This shouldn't be a thing. Alas, it is because applications can't or wont clean up after themselves.