If this isn't just an artifact of the way data was collected, I suspect it's not because Linux users are more likely to install alternative launchers, but because they're much less tolerant of non-FOSS software in general.

Anecdotally, most Windows users I know use a custom launcher, but they use proprietary ones like CurseForge or Feather (both of which show advertisements; something no self-respecting Linux user would accept, but which has been normalized in Windows).