If he's with you and not her, surely that means something.
I am sure you'll have doubts for awhile, maybe forever, about any guy you're with liking cisgirls better, but if you get all worried all the time, he'll sense that and that will cause trouble in the relationship, because he'll feel that you don't trust him.
A lot of guys have little things with waitresses if they're a regular, they may joke around with them, but it often doesn't mean much. (My mom used to joke around that my dad had a girlfriend at the coffee shop, but he didn't and she knew that, it was just a running joke between them). If you're very concerned, you could try to see if he'd be willing to go to another restuarant, but I don't think that's the answer.
But, now that the waitresses have seen him with you, that should give them a good signal that he's taken. And, if he did want to continue on a flirtatous relationship with them, he wouldn't have invited you to go to that restaurant, he would just keep you secret from them.
So... I really don't think you have much to worry about. 🙂