Bumpstops shouldn't even be a question. Those need to be set up to prevent damage to other parts regardless of the fact if they also act as spring retainers. Backs should be extended from the top, fronts from the spring pad.
For most people, the axle is limited by the shocks compressed and extended lengths. So my question is, why are you running a shock that allows that much droop? Once the coil unseats you no longer have effective traction on the tire. So anything past the spring unloading it's pressure is useless, potentially dangerous, and definitely a hassle when your spring drops out. Also, with that much droop, you're almost certainly loosing up travel. If you find a shock that has an extended length that allows your coils to still be retained, problem(s) solved.
Technically, limit straps would work. But I'd do some thinking on the shocks before I strapped the axle. If you're already losing potential up travel, while not using all of the available down travel of that same shock, then why do would you keep it installed?