We did a trip to Australia on a DL650. It had a stock suspension. Yes, it was very short on ground clearance. We did bottom the skid plate many, many times, but mostly on the big speed humps.
But even if it had one meter of ground clearance, we probably still wouldnt have gone much faster on the bad bits. The weight on the bike 2-up was a much bigger problem. Actually it wasnt such a big problem, as long as you didnt even try to go fast.
You can modify the suspension, and get some more clearance. In fact I would do some of that, if I would go again, the stock suspension is too soft, and sits too low with a heavy load, that means it cannot function properly. The 1000 might have a bit better stock components, though.
If you change the hydraulic unit(s), make sure you get something that lasts like the stock units do. You dont want to do much work on them during the trip, and they will be under stress riding 2-up.