garbageman, IMO you are absolutely right. That was the situation I was confronted with, I e-mailed devprograms@apple.com and got: "Please know that If a developer is NOT a member of either the iOS or Mac Developer Program, the developer may purchase Xcode 4 for $4.99 USD via the Mac App Store (this is a regular consumer purchase). All support for Xcode PURCHASES will be provided by the Mac App Store support team.". My problem with this scheme is that Xcode is not a mere "app", as I have already stressed in another post on the topic Xcode via Mac App Store. I hope Apple reviews and improves the updating of an "App" like Xcode. The rigmarole can be confusing, and the download speed (?) is slow, real slow. Apple might want to consider that, once the user as paid for Xcode 4.0, installed it, an update like 4.0.1 (and more to follow?) should be available through Software Update, and not through Mac App Store.
By the way, when MacOS 10.6.7 was available, I used the combo update.