This was suggested to me through the org-mode mailing list: replace ‘org-tag-persistent-alist’ instead of org-tag-alist in ~/.emacs. I tried it: autocomplete works for both the local and global tag lists.
What company backends do you use? Remove company-files from company-backends.
company-files is an autoloaded interactive compiled Lisp function in
company-mode completion backend existing file names.
Completions works for proper absolute and relative files paths.
File paths with spaces are only supported inside strings.