I'm with you all the way in your quest for perfect alignment. I just refurbished a 66k myself, and have similar worries about not getting the final touches, especially the transport, right. However, after some real sewing with the machine I'm more willing to classify them as "test patch problems" not really interfering with normal operation.
As has been mentioned, with flatbed, straight stitch machines material is easily guided and turned due to narrow feed dogs. This will also limit their ability to transport material straight over distance. The slightest drag on one side will pivot it and change direction. In real sewing, where most of the time there is more material on the left side, there will be more drag. Either way, active guiding is usually necessary.
I just try to talk myself away from letting perfect get in the way of good.
Stay addicted, Stein