My understanding (and I'll freely admit it is limited 
) is that these settings are required to account for the funky geometry created by the realities of an EQ mount (and to lesser extent, Alt-Az mount). However, there still needs to be an initial alignment or synchronization between the mount and dome. That is what the "Sync to Scope" button does in AstroMC (Foster Systems). And I think that is what the SGP "Sync" button under Control Panel - Dome does as well.
I wonder if the AstroMC "sync" setting still has effect if SGP is slaving the dome (and the "AstroMC calculates Az" is turned off in AstroMC application). -I'll try testing this next chance I get.
DaveNL