The only other thing I can think of at the moment is that some of these keyboards present themselves as multiple HIDs to a system, so perhaps that is somehow contributing to why this works.
Not entirely sure, but
this may be the code for detecting access. You can see they've made extensive changes to this file, and from line 625 to 794 there seems to code for handling access to the debug menu. There's references to the escape key here, and also reference to a (disabled) select+triangle combo (active only if the emulator was built with the menu enabled option). If this is the relevant code it would seem to be have been intentionally done.
I may try and get hold of a Pi Zero as you can convert that into a USB keyboard and send whatever key codes you want from it to play around with this further if no one else makes progress in the next few days.