The book was an older mass market paperback which had been reissued with different cover art but the ISBN hadn't changed.  I went ahead and listed it by ISBN, it was wishlisted, they accepted, I sent.  I get a PM from the recipient saying that it "obviously" wasn't the same edition listed but "all right.  Thanks."

I sent a PM saying that it was the same, I listed it by ISBN, the binding type matched, only the cover art was different.  I went on to say that if the cover art is important they need to make a condition or contact the sender to make sure it matches.

My question...Should I have done this?  Should I have just let it go and not said anything?  Opinions?

I think you did the right thing.  When you post a book to your bookshelf it says it might be a different cover.  You did nothing wrong.  If they wanted the, say, flower cover and you had the windmill cover, they could have sent a PM saying "I'm particularly interested in the flower cover.  If your is the windmill, please let me know and I will cancel. Thanks though."

You did nothing wrong. 

I think most people aren't going to pm to ask if your cover matches what they THINK it should look like.

Ani K is right-PBS makes clear that for the same ISBN cover art may differ. So....that's the only response needed for the pm you received. Maybe the recipient will learn something new about how thing work here!

I would have responded.  This person needs to know that the cover art does not have to match.  If you don't tell them, who will?

I would have responded too.  Cover art doesn't have to match and the recipient needs to make a Requestor Condition if they want it to.