When the last guy put the intermediate shaft in it was a tooth off. Then instead of putting a large screwdriver in the slot and rotating it till it was right, he just rotated the wires and hopefully timed it correctly.
That's one option,for sure.
You can put the rotor in anywhere you want,then re-sync the wires,no big deal. It's easier to get custom-fit wires to fit tho, if the rotor is where it's supposed to be.