@bmjob , Hi
Your workaround is good but will be erased with each update.
A safer way could be to use "surcharges" (in french). You can find explanations here : https://forum.recalbox.com/topic/18803/tuto-les-surcharges-mais-avec-vous (in french but google translate can help you)
Shortly :
First : Create a text file called .recalbox.conf (with the point at start of the name) into your /roms/snes directory. Inside this file create a line like pisnes.configfile=/recalbox/share/system/configs/pisnes/my_own_snes9x.cfg
I have a doubt : pisnes.configfile=... or snes9x.configfile=... @Fishou , @Bkg2k or @acris could confirm.
Next and last : Create the file my_own_snes9x.cfg where indicated in the previous file with, inside, the same stuff as the original file except your modded MaintainAspectRatio.
This file will takeover in place of the generated one.
As both files are into your share directory, they will stay after updates.
You could even put the file my_own_snes9x.cfg into your /roms/snes directory (and change the path in the first file). In such a way, if you do a copy of your /bios /roms and /saves folders, for security or for a fresh install, your mod will follow.
I've done it for piFBA in my GPI-case for the same problem of aspect ratio and it works well.