i see that controller has an integrated 3-way mode switch, have you tried booting retropie with it in each of the 3 modes? have a look at this guide:
it might be the next step if nothing else works. also, this thread is old but may still be of help: https://forum.xda-developers.com/mad-catz-mojo/general/setting-c-t-r-l-r-retroarch-t2987569