jasondaigo truthfully, I don't know. What I do know is it's recommended to flash from the latest stock build. I do not know if every partition gets flashed with graphene, or radios, modems etc. When I first got my phone, it ran graphene perfectly fine but I went back to stock for a bit then trying to return to graphene the phone wouldn't ring. What changed? Updates I'm guessing. Some on the team here have said it was an upstream issue and nothing to do with graphene yet as I've said my phone worked fine on stock, lineage and calyx just not graphene...
I've been flashing phones since the T-Mobile g1, the very first android handset, every dev says clean install from stock so that's what I've always done. Is it needed? I can't say but what I can say if graphene says the issue wasn't with them but now my phone works, something fixed it.