If you're good in the dirt/sand then I know the hefty GS will get you through it. I heard of a rider that races in the Baja that takes a large GS out to Rampart Range and just spanks the KTM's & CR's.
If you are moderate or less- than I'll assume the GS will topple over. There appears to be some deep sand areas and very soft sand areas. I've seen pics of KTM's Adventurer getting stuck. I know I'd dump my GS, thus the 300lb-er DRZ will be the bike for me.

I can relate to the uncomfy seat. Any type of cheap seat cover including sheep skin and bicycle type shorts should help.

No route has been picked yet. We were thinking approx. 300-350 miles/day to get to the tip of Baja. As you know, the beauty of the dual sport is we could if needed, always jump on the paved Hwy1.

What kind of range are you getting on your larger tank? Do you have a DR650?

Are you riding in the 100,000 Ft. ride from Foothills in August?
How about the Colorado Freewheeelers annual ss1K?