To a certain extent the prefs are compatible. If you take your prefs form say Maya 2010 and try and use them with 2011 Maya will keep a lot of your custom setting and shelfs etcetera.
It will then tel you that your prefs need updating and will update them leaving your custom setting alone in theory.
I would not recommend doing this however as it will probably come back and bite you on the ass later down the line.
Dave 
From a readers' Q and A column in TV GUIDE: "If we get involved in a nuclear war, would the electromagnetic pulses from exploding bombs damage my videotapes?"