Actually, you can't even manually change the config file. It seems that jstest & emulationsation interpret one button as "0" but retroarch interprets that same button as "3". So yeah, you can fix button 10 by changing the config file to say "7" but retroarch doesn't like buttons to have negative numbers assigned so this doesn't work as a long term solution.
Many will say "buy a different controller." The Amazon is so far away. Also, the cost-benefit analysis of using a pi and retropie compared to buying something like the Allcade was that I wouldn't be needlessly buying things that I already had!