I've done some places repeatedly and there is zero evidence that I am *marked*. Best Buy comes to mind, since there is one just a few minutes from me. TVs, appliances, phones. I've shopped for each of those repeatedly at this store. If they had me pegged as a mystery shopper, I would almost definitely be getting better service, especially since (at least at that one), they always have at least a couple people working right up the front entrance, who would be able to easily alert the other staff if there was some mystery shopper wall of fame.
Of all the places I've done, there is only one where they *might* suspect (it's also just as likely that since there's a short rotation period for this shop that they just remember me and know I am a good customer).
As for an entree, side, and drink marking you as a mystery shopper? As a single person dining alone, what the heck else would they expect me to order? When I go out on my own, using the bazillion gift cards I have (I'm a teacher), that is generally what I order, as well.