I'm just curious but what do you mean by separating the pads? I unbolt the rotors, swing them back and remove the wheel, replace the tire and swing the rotor (with pads still installed) and I've had no problems at all ever. However, I'm in the habit of replacing the pads on motorcycles when I replace the tires but I've removed the wheels on motorcycles including my R3T without removing the pads from the rotors with absolutely no problems at all, let alone "injuring" them. You just have to compress the pads into the calipers a bit. This is the same procedure done when doing brake jobs on any vehicle - cars, trucks, etc. In fact, in almost all cases, you have to remove the pads after you've removed the calipers. You can, of course, remove the pads on the Rocket brakes without removing the calipers but I see no reason for doing that unless you are simply replacing the pads. Even so, I rather swing the calipers back to remove and reinstall them. I've done so many brake jobs in the last 54 years (when I turned 16 and bought my first car and motorcycle) that I couldn't count them and I've never damaged a single pad. I just did a brake job on my F150 and, like most vehicles, you have to swing the caliper back to replace the pads. No problem. On the other hand, many of those older vehicles had drum brakes. Even my 1969 Bonneville had drum brakes. If you've damaged pads by reinstalling the calipers with the pads already installed in them (if that's what you're talking about), I suspect that you may be doing something wrong. Could you possibly have not compressed the caliper pistons?
Sorry if I'm misinterpeting your post but I became curious when I read it.