Yes it will, as you're re-indexing the wires to the rotor position, which is the opposite or moving the rotor to match the wires. Correct per the manuals no, Does it matter? only when your ability to achieve the desired timing is limited as it is in this case.
There are a few vehicle's in which the '"adjustment swing" is limited and those have to be wired with the rotor "clocked" and "wired"per the book.
This one hasn't been or the V/A wouldn't be hitting the manifold Not trying to be a S/A just clarify for the OP and others