You don't align by the marks as they can often be out, they're used to measure adjustments after the initial alignment. Are you sure they're not aligning it properly and then you're undoing that by using the markers?
You'd expect the adjustment plates to be set to the same marker on both sides of the swingarm though wouldn't you?
Either way the back end felt much better on my ride in this morning now both sides are set the same.
Take it to a better garage?
I would but tbh I only use them for tyres everything else I do myself and they're a 30 second walk from the office so it's a case of me being lazy and their prices being half decent. I can live with having to line up the back wheel once or twice a year.

holy
probably for the best I don't think my neighbors would have appreciated that wake up on a Monday morning