We do this a lot at work also. For bolts that needed to be completely sealed, but also able to be replaced. Except at work, we use a semi-firm caulking, that is slightly darker then the material we drilled a hole in, and grind it flush. So in the future we could find the spot easily, and just scoop it out, or remove it easy to get to the bolt. And it doesn't matter if the bolt gets damaged, since the only reason to get to it again, would be to replace it anyways. But the bolt should be stuck for good, and the only reason for getting it out, would be because you stripped the heck out of it. And yes, use a filler. Or you could always use a painted LED lens cap, or a 1/2" hole cap that they use for bolt holes in carpentry. All of these ways will secure the bolt further from movement. You can even slide the bolt around in silicone caulking before threading it in, and THEN use a filler to fill the hole in. It will be more secure.
Personally... I am topping the holes off with Smooth Cast 300, then blending them in with sand paper. Just remember, to get a some cutters for your dremel to trim the bolt to fit your strapping, washer, and nut on the other side, then sand it slightly to make it level, and seamless so it doesn't bite you when you wear it. Might be a good idea to rub some black caulking on the finished strapping bolts after they are all assembled for extra comfort.
And bolting the armor to my body... Maybe. After all, I have atleast 10 - 15 pounds of metal in my body from implants, and other little things. Don't break your bones too much... Or at least over 23 bones. But hey, what can I say... I'm accident prone.