There will be a difference in pressure. In general, don't substitute magnum primers for standard primers. In the case of .44 Magnum, Speer retested Alliant 2400 powder for its latest manual and found that they got better performance and lower pressure with the standard (300) primer than with the magnum (350) primer that they had been recommending.
In general, use magnum primers for ball powders like H110 and Win 296. Heck, just find a load in a reputable manual and use their load data.