It might, depending on how the logic works for how its using the antennas.
I'd think they would both be equal using MIMO, but perhaps they aren't and indeed one is being used as primary. Maybe only one transmits, or one is used for management traffic, so if that's the one with the best signal then logically it would perform better overall.
You could try just one at a time, in primary. Then do the same in aux, and see what happens?
Given they do label them as Primary and Aux, it would suggest there is a difference in how they are used.