The conflict isn't with maemodder... Maemodder is the simpliest program ever written .. only pure bash (and a bit of python and zenity) xD

The problem are the custom packages , just like hildon-desktop, hildon-staus-menu anche hildon-control-panel.
The Community SSU neeeds you to have the original packages ... so everyone has installed the custom packages (even who has done this through maemodder) has to remove them