Q: Since magic weapons bypass armor DR, do they also ignore the critical hit negating properties of Armor Mastery 2, 8, and 10?

Yes, they ignore armor mastery 2, 8 and 10, just as they ignore all other masteries. I’m basing this on the fact that armor "provides no defense against magical weapons." (emphasis mine; p165 about chainmail)

Note that an armiger’s reinforced defenses class abilities allow his armor to be used against magical attacks, so I would give him the effects of that class ability here. If he has reinforced defenses, he should have a 50% chance of the best feat he has kicking in. If he has supreme reinforced defenses, the best feat will always kick in.

I can see a case for making the ruling going the other way, so if that’s what you prefer in your game, I say go for it. I’d also consider changing it if you were planning to use a lot of sneak attacking creatures with DR (demon executioners, for instance), since an overabundance of a threat you can't counter at all is not fun for the PCs.