Jared I believe that EQMOD is in the class of mount interfaces that do not like to by sync'd. This has caused problems for SGP/EQMOD users - and the normal solution is to turn off the mount model in EQMOD - which disables many of the features of EQMOD that give it good pointing accuracy in the first place. I don't know the details of how to do this - but there are many threads on getting syncing and centering to work with EQMOD and SGP - and I think you put EQMOD in dialog mode. A google search on EQMOD sync SGP gets many hits.
Thus EQMOD is like Paramount and other mounts in that Sync is intrusive - and in no way "generally better." It corrupts the mount model that is one of the valuable features of the mount software.
I would like to point people like EQMOD users to the "Scope Offset" mode of sgp centering - but it currently does not work. Please take a look at the issue with Scope Offset - because until it actually works, there is no way to center Celestron mounts well - and EQMOD users are forced to disable their mount modeling capabilities. I posted a recent thread on it in this forum with fresh results.
At the same time - I think that EQMOD users would be able to use the full mount model along with Sync Target - but I don't know if anyone has tried it. I believe this avoids syncing the mount during the centering procedure - and from my tests it appears to work as designed - but it is not a solution for Celestron mounts.
The entire centering procedure in SGP amounts to iteratively calculating a local fudge factor - and there is no inherent advantage in the mount doing that calculation. In fact - there is a big disadvantage because for many mounts sync does not behave in the simple way that SGP expects it to - and the best way for SGP to control how sync behaves is for it to calculate the offset itself and not sync the mount during the procedure.