There are some issues, but with a little theme tweaking and such, it would be SEAMLESS!
Just find something you don't use (I chose the Texas Instruments). In your Configuration tab, just select the emulator you don't use (I'll call it TI from now on). Now for the TI emulator, point to the Misfit MAME exe. It may automatically set up your other media locations depending on your setup.
Thats it... Force rescan and give it a play!
I think this is more elegant than batch files, at least for me, because I can't get them to launch individual games in MisfitMAME.
Now for the theme tweaking, obviously, you will need to redo the screen and images for the TI emulator and associated artwork.
OH YEAH!