It is possible to exchange emulators inside retropie manually. I did this and it works, following this post (and the next one).
But I think you mean to get it offically into retropie? As far as I followed some threads, chips version might become the amiga emulator of choice, when it starts to get major advantages over the currently used version.
Back to joysticks: I hope Chips will fulfill my request someday. But if there is no improvement during the next weeks, I might look at the problem myself, since I am software developer for 20 years. This is not exactly my playground, but I looked at the source code and already located the places that need to be changed: The init_joystick function and some gui code.
This should not be to hard. But for me it takes some more effort and time to setup up a working development environment. I’d prefer if someone does it, who has already experience with raspberry developement.
I never looked at joy2key. This might be another workaround with its limitations.