Here's the lame way I did it....
http://forum.arcadecontrols.com/index.php/topic,135430.msg1400493.html#msg1400493I'm sure there are better ways if you're more coding savvy, but I work with what I know.
If you make a change to the original, all you have to do is run the batch file again to update all games of that resolution.
Note the tabs along the bottom. (seems you might have to click on a cell in the spreadsheet to get the other tabs to show up)
A lot of the resolutions are already there, but not all.
Ignore the "calculators" tab. I was trying to make a formula to calculate the correct theoretical settings, but they all looked like crap on my large monitor.
I renamed the ini with the desired settings (the one I used for experimentation) to the resolution just to keep things straight (i.e. rename mspacman.ini to 288x224.ini)
You could just have it copy whatever ini file you've made the changes to though.
Just remember to delete it from the list before launching the batch file.
EDIT: Keep in mind that thread is from 2013 and HLSL options could have changed since then.
I was using MAME v.146 on my cab at the time...and still haven't updated.