If you are loading some of the older, slower burn-rate Hercules/Alliant powders, such as Herco or Blue Dot, I would recommend using the large primer/large primer pocket case combination. These are not ideal for 45 ACP, and I believe (not an expert), they would benefit from the greater brisance at the base of the powder charge. Also, there are about 6-9 decades of load data developed around the large primer for some of the older and less popular extruded and flake powders.
Years ago, some of the foreign ammunition manufacturers used small pistol primers on .45 ACP as their standard. IIRC, PMP (Pretoria Metal Pressings) of South Africa and Fiocchi of Italy did this, and they still may do so. All of the American "lead free" .45 ACP used to use small primers. I am really out of touch, because I haven't bought new .45 ACP cartridges for at least ten years. In other words, I don't really know if small primers are the new status quo...
If you have a lot of cases with both types of primer pockets, you need to segregate them if for no other reason than load development. You might not see any significant difference with powders like Win-231 or Alliant Red Dot or Bullseye, due to their fast burn rates/low powder charges, but I suspect you will see differences as you go into slower burn rates/heavier powder charges like Alliant Unique and AA#5 (this is a grouping issue, not a safety issue). If you are using a single stage press like the Rock-Chucker, as you mentioned, you might as well get the full benefit of going slow and steady...
Bottom line: old data + old powders = large primers, at least in my opinion. To put this in perspective, I have a lot of old manuals and old powder....
EDIT: ...and LP .45 ACP cases....