Yes, your elite benefits will be honored. The only real exception would be that any changes you need to make to your ticket will need to be done through Amex, not US. However, that's not an elite benefit, just something you should be aware of. It's really no different than buying a paid ticket through an OTA like expedia or orbitz.

I know many on the forum would probably suggest not using your MR points for a paid US flight, but if it works for you, I say go for it. You shouldn't have any problems with your elite benefits.