Yes, it's not a big deal to remove a little material, though you should do so sparingly. I'd use a hand file for more control than a grinder. If I'm going to bother, I also ever so slightly, chamfer the edges. However before doing so, I'd make sure that if there are shims they are riding on, that those are fully seated, and if you had put grease under them to slow down rust, that there isn't an excessive amount causing the shims to not sit as flush as they could.
I can only assume that the caliper was sufficiently wire wheeled to bring it back to factory spec. If not then there is where the material needs removed instead of the pad.
At the same time, remember that a caliper piston produces orders of magnitude more force than your thumb can produce, so if you could get the pad in place correctly with only your hands, then it may not need any material removed.