The advantage of using eqmod pulse guiding is that all the signals to the mount motors come through a single interface so you avoid eqmod saying drive forward for siderial tracking while the st4 connection is trying to slow the mount down for guiding.
Here's some reference material from the author of eqmod....
http://eq-mod.sourceforge.net/docs/PEC_and_guiding.pdf
http://eq-mod.sourceforge.net/docs/EQASCOM_Guiding.pdf