Your reasoning sounds correct. We use at to show the location....so if I am visiting and I tell others my location I would say....Hey, I am at the zoo. You won't believe that cool animals. If I am in the zoo, it is like saying contained within the space so it shows that they are not just stating location, it changes the meaning. The number of species in a zoo are all the ones that can be found there. It would also be common to say, "We can see many animals at the zoo." It just changes the emphasis of the sentence. This one is focused on location again. Prepositions are tricky. The best suggestion is to learn the rules and check understanding (like you are doing now) but also remember we change them and use them in other confusing ways sometimes too. The more listening practice you have, the more comfortable you will be using them. :) Good luck!

If you are in the zoo, you're part of the exhibit: usually an animal, but you might be the butterfly house or the platypus cave. If you are at the zoo, as Brookie said, that's where you're located. You could be an animal in a cage, or a visitor or zoo employee or someone who wandered in by mistake. You could also be the ticket gate or the butterfly house. Since the zoo animals are both "in" and "at" the zoo, people talking about them sometimes unconsciously use "at," perhaps in order to avoid the reminder that the animals are stuck "in" the zoo and can't leave.

It illustrates how precise the location is. If you have arrived at the parking lot of the zoo and someone calls you and wants to know where you are, then you say you are at (around) the zoo right now. But if you are already entered the zoo, your response will be "in the zoo."