Lord Sessadore
Explorer
Come at it from a different perspective - the process of making armor masterwork doesn't have to occur when the armor is first crafted or forged.While you're right in that all magic armor above a certain point is masterwork, technically you can't transform standard plate into godplate.
I know there is no price issue or power issue or balance issue. But still, masterwork armor is not defined as a layer on top of the existing armor. It's defined as armor made out of a completely different material.
I realize this is all very easy to ignore, but the rules should really clear up this mess. If you enchant a standard suite of plate mail, you would end up with a +6 plate mail (which I agree would suck).
[/NITPICK]
Here's how I interpret what the PHB says on masterwork armor: Once armor gets enchanted with enough magic, the magic actually permeates the physical material of the armor. In order to enchant something to +4 or +6, you use those techniques mentioned under each armor type in order to suffuse it with the necessary amount of magic to provide that extra protection.
AV does throw a bit of a wrench into these works, admittedly. If you assume that the lower level masterworks always existed then it isn't much of a problem, but if you allow both the PHB default and AV masterworks to co-exist (for example, you can get either +3 plate or +3 Gith plate), then things get sticky.
Also, with the variant masterwork armors presented in AV (ie - that there is more than one kind of masterwork armor for a given enhancement level) think of it as no different than the choice between Dwarven or Razor on a suit of Scale armor. When the enchanter performs the ritual, he chooses which masterwork property to convey to the armor just as he chooses which 'normal' magical property to convery to the armor.