The answer to your question is no, all bonuses weren't unique to this rally. The vast majority are, though. The Gerlach bonus is on many rallies, there is a shrine there on Guru lane for Iron Butt riders, so it's included whenever possible as an homage/tradition. Even if a location has been used before, it's likely that a different question may be asked, just so someone can't fill in the sheets with something they already knew.
But keep in mind, people are recording their mileage and time at each and every one of the bonuses they are going to, so they pretty much have to ride to exactly where they say they are riding to. (Or be awfully good with a chassis dyno that can simulate mileage and have damn good satellite photography to zoom into plaques and such).
But what sets the rally veterans apart is that they know that it takes X time to get from Alturas to Tulelake. And they know that getting through Leggett will take forever. So even if the specific bonuses are brand-new, the towns can't really be that new to someone who has been riding around in this area for decades. And by the time you get to where a bonus should be, more often than not you can find it quickly. This isn't a scavenger hunt where things are buried 500 yards from the main road under a bush and you have to search for hours. (though it feels like that sometimes). Generally, if you get to a bonus location, you'll be able to find it.
