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.