Hi Mike,
the users are definitely available - although they will default to no-access for the new area. That's not so hard to change by hand
by a supervisor and the Operators list, (or with a few lines of hand-code) if you like.
One of the things we discovered with "auto giving existing users access" was that it seemed like a good idea to save time when the web bit was first introduced, but as the people using the windows and web parts started differing it because unwelcome. Indeed the very idea that Windows users had automatic web access, and vice versa, became a hindrance not a help. (so we changed.) It's very "hard" to change an area name though because obviously existing clients have access set up on the old area name. So it's something that's worth thinking about up front - it's a lot easier to get it right now than it is to change it later on.
Unfortunately hindsight will likely prove you wrong which ever approach you take. There are benefits, and disadvantages both ways, so inevitably at some point you'll think "hmm, if only I'd gone the other way". On balance I'd use different area names if only because it's more secure. And ultimately that's a good goal to aim for.
cheers
Bruce