They can affect accuracy in several ways,Using myself as an example but knowing other people have experanced the same.
My system one 54 cal. barrel loads smooth and ease works well with #11 or musket cap but when I got the conversion to 209 the groups openned right upthis gun shoots 4.5 inch groups @ 200yd with musket caps with 209 some group but some will be a foot away.I was using 777 aty the time it has a higher ignition temp. and I think it was moving the sabot some befor the powder ignited,to check I loaded with out powder and measured the location of the bullet and sabot, when I fire 209 it moved an inch. The 50 cal barrel for that gun has the same problem. My new Omega is tighter and I am using APP which is the easiest of all except black to ignite and it will shoot sub one inch groups with winchester 209's.
It is one of those things where a lot of other factors can change it. Lee