the oil pump mark and bottom timing mark will line up the same, its just more accurate with the balancer (assuming your keyway isnt flogged) as it has finer marks closer together. the ideal way to set cam timing is with a dial gauge down the spark plug hole of cyl 1, but its not practical if you dont have one.
if both alignment keys are there then its not possible for it to align wrong, the key is beveled to guide the cas onto the right teeth if inserted slightly out of alignment. if its inserted way out of alignment it simply wont go in and forcing it will just break the cas.
99% sure power fc doesnt have any trigger angle correction as its an application specific ecu (ie, plug and play).