Is a clean Mac upgraded to Mavericks as good as one with it pre-installed? I've just bought a new Air, from my local Apple Store, only to find that it comes with Mountain Lion!

Should I return it for pre-installed one, or just let it upgrade?
You could do a clean install youself after formatting the disk.
You will end up with exact the same result after doing this.

Why the format, you ask?
You won't have any Mountain Lion files on your system.

Returning to the place you bought it from is as easy, you say?
Returning the device to the store does not make any difference except spending (more) time and probably pay gas for the car.

If you let them do the update, they will just click the icon in the AppStore resulting in the same result as doing it yourself. (This does not count for an official Apple Retail Store, but it does (at least in my country) for the premium resellers)

Official Apple Retail Store
If you have an official Apple Store, it comes as free service to get the OS X re-installed.

The only difference that would really help you out is getting a newer replacement from the store, with Mavericks pre-installed. I doubt they will replace it as the device isn't broken and cannot be returned for RMA.