I think that string-thru-body holes are sufficient, although it totally sucks what happened to Chris_Lohman's mockingbird body. If you're going to pay a lot of money for a body, it sucks that it has errant holes that had to be plugged, regardless whether or not the new bridge covers them up (although much better if it does). Warmoth customers are a picky bunch - that's why we come to Warmoth in the first place!
Drilling your own mounting holes isn't that hard, but it sucks having to do it with a hand drill. I've done it with 'okay' results, although I would've liked a drill press. What you can do is take a tiny dowel rod and cut it into six pieces. Put the odd hardtail bridge on the guitar, and stick the little dowels through the holes in the bridge down into the string-thru holes in the body. Provided the dowel is a snug fit, this should keep the bridge in place and let you drill holes using the bridge's mounting holes as a guide. I never used the word "holes" so much in one paragraph.
There are a ton of good hardtail bridges out there. One of my favorites is made by Mighty Mite (ducks thrown object), and it's really affordable.
http://cgi.ebay.com/Chrome-MIGHTY-MITE-Hardtail-Guitar-Bridge-Strat_W0QQitemZ350092537279QQihZ022QQcategoryZ41407QQssPageNameZWDVWQQrdZ1QQcmdZViewItem
I've never used one on a Warmoth body but I've played other guitars with them and they're very nice. I also think that Might Mite's cast bass bridge is every bit as good as the TK5 Warmoth offers, at half the price.