Kauco, I have no idea why there are holes in the head that don't mate up to holes in the block..............but it's a common thing (don't concern yourself with it). Obviously it's had those holes since the beginning and has probably made it well over 100k miles like that. Perhaps having a hole there lead to a blown head gasket, or perhaps it was just a coincidence.......who knows. It doesn't really matter as there's not really anything you can do about it anyhow (at least that's my logic). When doing a head gasket focus on looking for things that aren't normal (like cracks, warped surfaces, leaky valves, worn guides, etc). If all that checks out okay, put a new OE Toyota gasket on and feel good about it. As a technician for Toyota I've done lots of head gaskets and never had an issue with those casting holes and/or gaskets not having matching ports. As long as you're using quality OE parts none of that should be an issue. Good luck. Tim