Hi John,
Your situation is not strange at all. Licensing is just complicated. We’re trying to make licensing affordable for small-scale users with the 10 domain server license, while recognizing that a server with hundreds of domains on it may only be billed at $5 per domain per month (I know a fellow that hosts 780,000 websites on 12 servers with 12 Squid servers in front and 3 EMC file servers in the back–he’d get a mighty good bargain with the Unlimited Virtualmin, but then he wouldn’t use the vast majority of Virtualmins features because of the type of websites he allows).
There’s really no perfect solution, but if someone opted to buy the $80k server just to beat us out of buying a few more Virtualmin Unlimited licenses they’d probably be penny-wise and pound-foolish. It is expected that most folks will have a variety of server sizes with a variety of domain needs which is why there are many price-points offering a variety of domain sizes. The proprietary leader in the field (cPanel) is a flat-rate price point, and so we’re trying to be more flexible than that. Some folks are just going to come out ahead in any licensing scheme, and we’re trying to offer enough options so that most folks can pick something affordable. To counter your big server example, an application service provider might host only 5 domains per server and so only need the Virtualmin 10 bundle, and yet they charge $300 per month to host some application for Fortune 500 companies…As in your example, they’re getting a bargain, but there’s not a lot I can do about it…I’m not going to police how much folks are billing per server. 
We are offering bulk licensing for situations with many servers, however, and we don’t want anyone to have to think about licenses. We’ve written a license manager that is as unobtrusive as possible and as helpful as we can manage with regard to making sure you get the right license on the right box (and you can upgrade it at a cost of the difference in plan prices if you find one box gets more domains than you anticipated, though that isn’t available in the shop yet). You can also change from one license to another by changing a single file.
If you’ve got more than ten servers, or if you’re buying more than five Unlimited or 250 plans, you’ll be bumped up into the Partner category, and you get discounts on all purchases, including the purchases that bump you into the Partner program (though that discount is currently applied after purchase as soon as I’m aware of it, not while you’re in the shopping cart…but I’m working on making it all automatic). Once in this group, you can use a single license file for all of your servers–the license manager will of course flag abuses and suspected abuse–so your fear of keeping up with licenses is probably unfounded. You will have to keep up with how many machines you have running Virtualmin Professional, so you don’t end up with one or more disabled machines, but pretty soon you’ll even be able to login to Virtualmin.com to see how many servers are active and how many domains you have free on each. We know this is a concern for large-scale hosting providers with hundreds of machines, and we know that the competition do not provide a good solution to the problem.
In short, I feel your pain and we’re trying to address it. Whenever we talk to hosts using one of the other proprietary virtual host management tools, we kept hearing about licensing problems. Mainly just ornery treatment by the vendor and a dislike for the heavy-handed compliance monitoring, but also a lot of “I only run 20 domains, but to get cPanel I have to pay $450, plus the cost of Fantastico”. Of all of the licensing schemes out there, the “domains per server” model was by far the most popular (though everyone would rather have it for free, of course!).
I’ll do the math on more multi-pack type plans, including the 50, 250 and Unlimited packages for multiple servers with a quantity discount built-in. Perhaps this will help with situations like yours.
We’re trying our best to give folks what they want (while still paying for all of the development we’re doing to make Virtualmin Professional the best hosting platform in the world).