I think that the "Transit screws" are used to lock the moving armiture that the laser lens traverses above he cd into place so that it doesn't get jarred out of alignment. This prevents the laser from reading across tracks instead of along the tracks.
It actually is very important to use the screws to lock down the parts because when the laser gets out of alignment, it can cost a hundred to a few hundred bucks(or more) to have a tech fx it.