Apple - Is it okay for a brand new 13" MacBook Pro Retina to not sit flat?

If a unibody Mac is wobbly, I'd have it serviced sooner rather than later. The tolerances inside are crazy tight in some cases, so a warp could cause subsequent damage to sensitive and costly parts. A trained technician can tell at a glance if the damage was external or due to manufacturing issues.

Now, that being said, I've seen dozens of Macs where people reported they were off and most were the table it sat upon, and not a bend in the unibody frame of the Mac. You can test by measuring how many sheets of printer paper fit under the leg(s) that has(have) a gap.

Then rotate the Mac 1/3 of a turn and repeat the measurement. Then take it to a second flat surface and do the measurement one last time if you're not convinced that it's the frame instead of the surface that is off-level.

Any wobble that's less than three sheets of paper is probably nothing to worry about, but what if you needed a logic board repair 10 months down the road and today, your Mac is bent out of tolerance and you were denied warranty coverage since you didn't report the bend until then? Only by getting it checked will you know if yours was out of tolerance and have a service record to point to in case of a warranty repair question later.

Are you sure your table/desk is actually flat ? Did you test it on several surfaces ?

If yes, then I'd go to the Apple Store and had it replaced. This is a premium machine and it should be of good factor. I bet the genius will exchange it or have another one commanded for you if you don't have a standard configuration.

Check the Battery!

Late answer, but could be really important to someone: I was recently given a MacBook Air whose base (and top plate) were severely "distended" (that's the best word I could use to describe it).

Upon opening the case, it turned out that the battery has gone bad and swollen up like a wood tick on a hunting dog in August: I'm personally surprised (and grateful) that the battery hadn't started leaking or exploded.

The good news is that it was easy to find a replacement battery on Amazon, and it took about 10 minutes to replace.

Most astonishingly, the case returned to its sleek flat self after replacing the battery, and the MacBook Air now works perfectly.