I chose to go with MALA for ease of use. (not to mention the great write up by UncleT)
When I was trying to decide which FE to use, I read a lot and people mentioned that with MALA you did not have to mess with ini files.
To clarify, you don't have to edit .ini files to set up mala. The Ini's still exist it's just that they get changed by the pretty MaLa gui
I assume this tool is just a easy gadjet that creates individual .ini files for each game, setting an appropriate resolution.
If you plan on having separate .ini files for each game then mame will look at those for sure. I have a few games that I have made separate ini files for as I want them to run a little differently, and all works well.
By the way there is no reason why you can't have MaLa and MameWah on the same PC (I have that and Atomic too)
I plan on using an arcade monitor when my PC monitor breaks (and the wife lets me buy one)
If I go to the trouble of installing mamewah and use the mame resolution tool to configure a bunch of ini files to make my AVGA & Betson combo look good, Is MALA going to recognize and use them?
Swindus uses an arcade monitor
Anyway, to answer your question I can't see why that would not work.
I just had a look at it and it looks like a very nice tool.
But to be sure, just have a go and use the tool to set up a few games and try it!
Nothing to lose!