The simplest way is a dab of hot glue. It's easy to apply, bonds to the vinyl pretty well and if you fill it too much, you can shave it off with a razor after it cools.
Hot glue won't hold over the rooting; I've tried! I ended up just giving my girls high ponytails, which fit their style perfectly anyway. If you want to try plugging the hole, I would try coating a little bit of cotton in mod podge, sticking it in, letting it dry, and then covering the remain with it. Sand afterwards, and I think it should work! I've covered the holes on Barbie heads this way, but never on such a big hole.
I've heard that you can just root around it. That's what I'm attempting right now with my three-eyed-ghoul.
The best thing to fill the hole with is Epoxy Sculpt. It's a two-part polymer you can buy at your local arts and crafts store. After applied, it can be sanded to be flush, and painted afterwards. If you plan on leaving the heads bald, this is the best method.
If you're going to be re-rooting the head, don't worry about covering the hole, because the hair will cover it!!! If you're looking for the easiest way to change hair without re-rooting, I'd recommend the LIV doll wigs. Hope that helps.