Not necessarily, especially if you aren't at maximum pressure. The 45 ACP has lots of case capacity so any fluctuation between the primer sizes may not even be noticeable.
There's probably two schools of thought, depending on what you are trying to achieve. If you are loading for maximum accuracy and precision, I would work up a load with both primers to see what is best with them. There may be no difference.
If you are loading more "plinking" or practice ammo it probably doesn't matter.
In either case you are going to have to separate brass by primer and load them in lots so maybe working up a load for each isn't really a big deal. I will separate and load all the brass then only take large primer ammo to the range until it's all used up. Then it gets processed while I am shooting small primer ammo. Eventually you get to the point where you don't have to spend too much time sitting in front of buckets playing Big Primer Little Primer.