Yes but it'll have the same issue.
Here's the deal.
J5 is used three ways:
Always on (on a second screen).
Toggeled between mame (via ahk).
Called manually and exited when done (like in a fe or something).
Now for the latter adding joystick support is simple.... just add the old winapi in and you are done.
For the other two, however, it causes complications. See via the winapi method, which causes the least overhead, joystick status is always read and acted upon, even if the form doesn't have focus. Which can cause issues to say the least. There are ways around it, but j5 is used in so many different ways it is "safer" for me to leave it out. Directinput is also an option but it chokes when another app has also wrangled the joystick, which would probably be the case as well.
I'm not saying I won't add it, I'm just not going to add it yet.
An ahk script would work, but it'd be constantly polling the joystick status and thus would have to be closed when j5 is closed.