As an aside, FSM procedures are always written as a compromise between the original design specifications and the available repair methods. When writing these FSMs, Toyota expected their dealerships to be able to do a lot, which they typically don't (for reasons of their own). While it's perfectly reasonable for a dealership to be expected to have all the tools and methods necessary to perform any and all repairs on a Camry, Land Cruisers were intended to be used, and available for use, in extremely harsh environments, which means that the expectation was that when they failed, they likely wouldn't be near a dealership with access to all the gee whiz stuff we have come to know and love here in the land of opportunity.
Milling heads has long been an accepted practice, and I'd bet Toyota knows that. Either they didn't allow enough wall thickness between the lower side of the bottom galleys near the bottom surface of the head, or they didn't think that machine shops would be readily available and replacement parts are certainly easier to deal with than machine work. I would have to think long and hard about dumping a head that was 0.002-inch over the warpage limit. It would certainly be interesting to see a trashed head milled in 0.005-inch increments to see exactly how much meat is available on the lower face.
Maybe
@Onur has some insight on this.