At any other restaurant I would tell you not to worry. My last two visits to San Angel have not impressed me with their customer service, it's also noisy and dark in the place and I would be hesitant to go into the place knowing I have a special request.
To be fair, they will probably treat you just fine, I'm just less sanguine about that being the case as I would be if discussing almost any other WDW restaurant.
To get what you want from them, I would plead a slight digestive upset and request a double sized Cheese Quesadilla while pointing to it on the menu.
It seems silly, but on my last two visits I had to argue (really too strong of a word) with the waiter because I did not want Queso Fresco on my food. That's all. Please no sour cream or guac, and please hold the queso fresco. "But sir, it really should have the white cheese on top..." Please no. "But, but, it has hardly any flavor. It's very mild..." Then I won't miss it. It was like the guy owned stock in the cheese company.