A domain name mapping question

In a previous post, I mentioned I was migrating a bunch of existing Web sites into WordPress MU. In this question, I'm curious about some domain management decisions.

Each site has its own well-known, unique domain. For our purposes, let's call them DomainA.com, DomainB.com, etc.

I like the idea of configuring WordPress to use subdirectories, because that's a lot less hassle for DNS setup, but I'm going to want each of those unique domains to go to their own unique blogs.

I'm guessing the right way to do this would be to set up WPMU on its own master domain, say master.com and then use the domain names as subdirectories, like:

master.com/DomainA/
master.com/DomainB/

Now, here's the question. I can certainly convince Apache to map requests to DomainA.com to master.com/DomainA/, but will doing that confuse WPMU?

Is there a better way to think about this?

Thanks,
David