Quoted from phishrace:Technically, yes. The idea was that you put a toothpick (or awl) between the bat and the flipper rubber, then raise the playfield to finish tightening. Nothing moves.
Those that choose to align with the lane guides instead are just making the game easier. Of all the hundreds of holes in your playfield, those two and probably the most precisely positioned. The game designer put them there for a reason. That is how the game was intended to play. Unless your lane guides are hammered, there's no reason to ignore the alignment holes.
Unless they are completely off which they often are? If you enjoy inducing flipper hop to get what you believe is the "designer intended" flipper feel, then sure, go ahead.