i guess what i'd do then is have some batch scripts available on your desktop which you can run which would swap out mame.exe with the other one whenever you wanted.
Thinking something like this:
2 batch files on your desktop, each one just copies mame.exe into the mala folder from your 2 different builds. let's call them 1.bat and 2.bat
launch mala, run it in a window
run 1.bat
select a game from mala and playtest it
exit game
run 2.bat
pick same game in mala to play it now in the other version of mame.
that way you're not forced to switch lists in mala to check out the same game in a different version of mame, which would be time consuming. Now you've got one list and just one configuration but an externally controllable swapper to let you experiment.