The original basic PAMCO does not have an issue as its ground is from the mounting screws for the PC board as well as the black ground wire. The same PC boards in the XS650 PAMCO are used in the Honda CB750 PAMCO ignition and that system is crank based, so the wires have to go all the way from the bottom of the engine to the coils.
The E-Advancer is a little different as the black ground wire serves as a ground for both the high current transistor driving the coil and the more sensitive MCU, so you should splice into the black wire closer to the blue box to provide a ground closer to the blue box but it is also not that critical because there is a ground from the engine mounted sensors coming the other way to the blue box.
In any case, using a heavier gauge wire for the extensions as suggested by glenpm is a good idea to reduce the possibility of having a problem.