As @Substring said, in RB 4.0 the custom pin config is not yet implemented. You'll need to recompile the mk_arcade_joystick_hotkey module in its last release to get this feature.
@turtlezza I assume you are asking if you need a Bluetooth dongle to use a PS3 Controller, providing that controller is connected to the Raspberry Pi via USB wire?
If that's the case, then no. You would not need Bluetooth in this case.
@aubrey Just to make things clear : it is online for the purposes it was meant to. Being a supply of 4.1 builds is not yet among its tasks. Please be patient, as we will be ready to support the 4.1 once we solved some problems first. Check out recalbox announcements !
We won't do any support of 4.1 as long as we haven't released it as unstable.
I was having the same issue with my pi3 and noticed that when I rebooted without my ds4 controller plugged in, I had sound. I'm not sure if it is just a coincidence but it has already worked for me twice.