If there's one thing I've learned from here, it's stick with the plans. The suggested driver for the AT is $35, not exactly a dealbreaker for most people.
We are not assimilated into this thinking (I'm relatively new here) and we're not paid to endorse these. Bill certainly doesn't have any magic Kool Aid, and even if he did, I'd bet he pick some nasty flavor like Orange or something

Sticking to the plans just makes your decisions far easier, and the results are spectacular. The only real reasons to deviate from the plans are if the drivers/parts aren't available to you... or you absolutely know what you're doing. In the second case, you probably wouldn't need to ask any questions here, and would be designing your own speakers.
As far as the box goes, it's just a box. Add on whatever you want to it. If you want the little shelf on top like Mr. Webbers, just add an inch and a half to the vertical dimension of all the side panels. That's actually a modified version of the AT, called the Tall Auto Tuba (TAT). Just make sure it all fits where you want it to. I believe the dimensions of that box are somewhere around 20"x20", with the minimum width being around 12".
The recessed letters are just a jig with a router. I'm betting Nimrod made his own, but there are sign making kits available in woodworking shops.
http://www.woodcraft.com/Product/202014 ... gnPro.aspx
As far carpeting, you can't carpet it and do the letters... unless you have x-ray vision.