I ran into this behavior by accident and it seems quite unusual to me.
Why do Emacs Lisp regular expressions match the percentage and dollar sign as word characters?
One theory I had was that this is because both of those signs are valid in function names in Emacs Lisp but ^ seems also to be valid in function names and doesn't match.
(string-match "\\w" "%") ;; => 0
(string-match "\\w" "$") ;; => 0
(string-match "\\w" "^") ;; => nil
What syntax category a character belongs to depends on the major mode: in text mode % has syntax word but in say C-mode it has syntax punctuation. What you want interpreted as a word varies depending on the "language" of a buffer (which is partly reflected in its mode - that's why syntax tables are mode specific): the syntax tables try to account for that, not always satisfactorily from every POV, but they provide a decent compromise (and one which you can modify - with care). See Syntax tables in the Elisp Reference manual.
E.g. in text mode, when you write "I am 100% certain that this is a bug", you probably want forward-word to go past the % sign: the 100% is a single "word". Similarly in "I paid $2.00 for this lousy coffee?", the $2.00 should be considered a single "word".
IOW, it has nothing to do with what characters can be used in function names in Emacs Lisp.
