I generally wrap a rag around the dropper post and clamp over that, and avoiding putting big forces on the bike in the stand. However, if there's enough hose and seatpost left, I feed it back up into the frame, (sometimes undoing the remote to do this), raise the seat post enough to clamp properly over the lower half. Never clamp a frame directly; it's unprofessional, can damage paint/decals/risk crushing thin tubes which aren't meant to take that kind of force, etc. Just the way I was taught.
If it's got a dropper post, it's more than likely got a pressfit BB thesedays, so you generally don't need to reef things as much on modern MTBs to get them undone.