You can 'upload' a file into a completely local web app just fine. The directory access is only necessary if you need the web app to be able to spontaneously write back to the original file on your machine, or if you want to read a whole directory tree, which might be slightly convenient for things like gerbers but can easily be dealt with in other ways (especially with gerbers, which you can distinguish by filename, something that the web browser does expose to javascript).

(and I do think it's kind of irritating that Mozilla is fighting against such useful features on somewhat patronising 'the users won't understand what permission they're granting' grounds)