Welcome to the forums, Butlermilitia!
Let me start off by saying "I am not a lawyer" so any advice you get from me...you'll be getting what you paid for it.
As for the legality of the surplus store selling those military MREs, that's always tough to say. There are MREs that are legitimately out there...such as MREs given away as disaster aid. I've also seen MREs starting to be officially "surplused" by the government - as in, the govt. sells them to dealers who are authorized to resell them to the public.
But on the other side of that coin, the govt. is still known to go after surplus dealers near military bases who are selling MREs they got from servicemen.
Personally, I get the feeling the govt. is starting to change their tune from "commercial resell is prohibited" to "commercial resell is prohibited except when we say it's ok". And how, exactly, you're supposed to be able to tell a legit resell from a non-legit resell is anyone's guess.
As for that wording, maybe a lawyer amongst us can explain better, but to me, just because someone puts wording on something, doesn't make it legally binding. If I sell you an empty box and write "you can't resell this" on the outside, does that mean you're breaking the law if you resell the empty box?
More to the point, and back to MREs, if there are no other ways of obtaining MREs except by appropriating them from military sources (soldiers, etc.) and all those means of appropriation are illegal, then it might not be a stretch to say that all military MREs you see in stores are illegal.
But that's not the case...at least not anymore. With MREs being used for disaster relief and being officially surplused, it's no longer the case that military MREs can only come from the military illegally.
But you still have to be careful. Check out this thread on a govt. investigation into MRE sales on eBay back in 2005:
viewtopic.php?t=612
Just because some MREs are legitimately obtained, that doesn't mean you can't still get caught with illegal ones. I've heard from at least one eBay buyer who got a visit from Army CID because he won an auction of MREs that were later determine to be stolen. And yes, they did confiscate his MREs.
I'm not trying to scare you off all MREs, I'm just saying the case isn't clear cut for them being completely legal or illegal. If you buy some at a surplus store (for their inflated prices), you're probably going to be safe enough because that transaction is fairly anonymous. On eBay, you just never know.