on the different keystrokes required for a different emulator - with an ipac, can you set up a batch file to reprogram the encoder via winipac for the other emulator when the game is called, then reprogram back to mame (and mala) keystrokes on exit? in effect a wrapper?
I know you're probably using Mala Tree and I don't know how to hide branches on the tree like you're referring to. I would just save a different version of mala with a different tree without those emulators.
for example, I have a version of mala I run that has some things I hide from casual users - like a full mame gamelist, etc with no audio, video, or intro video, for troubleshooting/maintenance purposes. For guests I would just run a different version that doesn't allow switching to those gamelists and with the bling turned on. Sometimes I just go to options and change/delete the keystrokes that let you switch gamelists, leaving them stuck on the gamelist I want them to use. for example, on my non tree layout, up and down scrolls the list while left and right change lists or emulator/lists. I.e. there is a list that is just daphne games. I just turn off the left arrow and right arrow in mala and they're just scrolling one list.