When I first put the "mini-gen" on, I had to trim a bit so as not to touch the mag rotor. I took it for a test ride and noticed a small loss of power.
There was nothing connected to the wire from the gen. I just try on and fit new parts as I go. Then if I'm not ready with the rest of the add on, I take it back off to use later.
I didn't think about the coil to much until you mentioned possibly canceling the ignition coil, it makes some sense being that the North magnetic field is cutting the ign. coil, while the South magnetic field is cutting the charge coil. Depending on the direction of the winding (cw or ccw) of the charge coil, and being an AC out put of both coils could create a magnetic brake. robbing some very needed HP (maybe?). Also if the out put electrical polarity were backassward of the two coils it might not run at all. (Don't think they would build something like that).
I know with my GT5 Racing, if I just THINK about using the white wire for anything, it would sputter and stall .
The GT5 comes stock with a two wire mag. I had a three wire replacement, now back to two wire mag. I got with the new
non-magnetic rotor.
I don't know enough about how the timing works in conjunction with the magnetic field(s) cutting the magneto coil, I understand the theory of creating electricity with magnets and coils, Just not the precision aspect (timing wise).