Derick didn't mention US/Mountain; I'm pretty sure he was referring to the country/region code US. I believe he is saying that removing this entry from zone.tab undoes the mapping between the America/Shiprock alias and the US country code.
I was initially concerned by this change as well, but as it seems that other aliases listed in backward do not appear in zone.tab, I don't think it's an issue. I think it's safe to say that aliases are presumed to be part of the same country/region that their linked zone is part of. (All the more reason NOT to alias across country borders, if you ask me...)