It is not clear from looking over the website, but since bottles appear closely related to Flatpak I am wondering if they support being installed to a different path than the default. Flatpak doesn't allow you to do this in a piecemeal way[2], but it does allow you to set up more than one entire Flatpak environment to different paths[3]. I'm hoping bottles can at least manage that?
[0] There are dozens of tools on my list for this, mostly around application and container management.
[1] I am a very vocal critic of the way Linux Desktop does things, but Windows is becoming worse at an alarming rate so it will probably be the least-worst option in a few years.
[2] A regression from features we had in desktop OSs since the 80s.
[3] Not that any GUI frontend for it pays attention to that. sigh