You would probably look weird at an software that installs itself in C:\MYAWESOMEAPPLICATION instead of using the Windows program folder like literally every other piece of software (except for legacy stuff like LTSpice). Creating visible directories in the home folder without asking is the Linux equivalent of doing just that.
Check if the XDG environment variables are set and store your stuff in these places — as it is now can be used as a last resort fallback. For reading config/data you do the same.