So your issue is that mapping.xml OVERLAYS button commands on top of what's already mapped (in case you want to use an external controller of some type, so GP2X buttons remain the same and external buttons do similar stuff). It actually explains that on the top of the mapping.xml page you linked! You would want to use confix.xml to REPLACE the current mapping on the GP2X. Further, there used to be a mapping command to specifically flip the GP2X buttons but it's not in the wiki and I'm not sure if it will work on newer GP2X builds. I no longer have a GP2X so I can't test it but it's:
<INVERT value="YES" />
"YES" to invert button A&X with Y&B (feels like gp32/lsdj). regardless of value, X always mirrors A and Y always mirrors B