Halion Sonic 3 has an almost completely different, much newer sound library compared to the Cubase Pro version of Halion Sonic SE (which has over 1000 more sounds than the Elements version), but the stock GM sounds are the same in all versions.
But you can replace the stock General MIDI sounds by following this super easy procedure:
You can turn ANY sound loadable by Halion Sonic 3 into a GM preset. This includes the sounds from HS SE and any expansions you bought.
For the best GM file compatibility, I recommend turning off any Chorus/Delay/Reverb insert effects used by the presets and then saving them under a different name.