Rod - in - pipes - always. Like Sharpsman says - HARMINICS (the big H must be the same, shot to shot)
If you want to shoot with the rod out of the pipes, develop your load & sight in your rifle that way, rod out of the pipes.
When loading the second shot for my first 14 bore moose, I just dropped the rod after removing it from the bore.
Time was of the essence, the shot was not needed quickly, but was needed.
The second shot hit perfectly, offhand at just over 100yards.
I would not trust that on a bullseye target when "ALL" of the BEANS are up for grabs.
There just MIGHT be a difference in poi or accuracy quality - so if interested in pin-point accuracy, one should do everything exactly the same.
This is all part and parcel with the "CONSISTENCY" rule.