It is the distance from the rear cone that you want. Cooper pipes work well but are measured different because the weld is in the middle of the band and not at the start of the rear cone. The front cone is basically just a collector for the reflected pulse off the rear cone.
Engine mods can decrease torque, if they do you might need a longer pipe to make up for the loss torque, or you can run a smaller prop and shorten the pipe to take advantage of the higher RPM allowed from the mod, there is no set in stone rules that you can apply across all the different engine builders. A good engine builder should be able to reccommend a pipe length for their motor and pipe combo.