Only in implementation internals? I'm fairly certain I've encountered it in other unexported package symbols in library code, things like struct constructors where you want a "smarter" "make-my-struct" function. But perhaps I misremember.
> What will you do if three or more modules want the same function name? Tack on %%, %%%, ...
Certainly not!
I think your points are all very fair: it would be a smell, and is evidence of a need for improvements at a more structural level. It just smells a little less than a seemingly purposeful misspelling to my nose.