Small hole in head at bottom of valve cover bolt!

That's exactly what I was going to do. Cut down a small bolt, put a notch in it and thread it down with red loctite. It won't go anywhere and no chance for it to enter the engine. I poked around with a small screwdriver and there's really no more material that can come off.
Don’t over think this. Many heads have this happen after porting. If you want to keep bolts for a stock look, use thread sealer. Just have to remember to apply sealer every time bolts are removed. If you switch to studs you can use the new orange thread locker on the studs and they will stay permanently sealed.
Just make sure you use some kind of sealer on the threads that go in that hole to prevent a vacuum leak.