I was pretty fortunate in that during my mock build everything lined up quite well, so definitively finding the centre line became almost redundant.

The neck fit on mine is quite snug, and positioning of the bridge PU in the middle of the routed hole was very close to ideal for intonation range and centring of my test strings over the neck. Only issue I had was in maintaining clearance around the bridge PU in the hole caused the entire bridge to be twisted slightly clockwise, so some slight enlargement of the hole was required. Enough was removed so that with the bridge assembly in the correct position the PU height could be adjusted without hindrance from the body.

If I were to establish a "centre line" then first I would loose fit the neck into the body and have it feel comfortably in the middle of its range of movement. Then I would use a 1m ruler placed down the centre of the neck and extend a line from there. For me the centre of the neck is most important and all parts of the body are only extensions from that line the runs down the middle of the neck.
If the PU routes are too far off that line then work needs to be done to either reposition the neck or the routes to be closer together along the same line. Remember that the "centre line" is your line that you are building off, so (within reason) you need to place it where you need it to be.