I've owned an 87 Integra, as well as a 94 Integra that were both serviced from dealers that I didn't buy from. I've never had any trouble with warranty work, including the replacement of transmission in the 94 Integra. I did purchase my MDX from the local dealer, but service was never a concern. At my local dealer, each department seems to be run separately, so they don't seem to care where your car came from. It's my understanding that they like warranty work, because Honda pays them pretty well.
-Aaron
-Aaron