When you have a barrel adjuster and a separate lock, of course you want the two together - that's what the lock is there for. But that has nothing to do with the 1mm clearance between the end of the indicator chain and the axle end. You could have the barrel adjuster way out of position (too much or too little cable tension), have the lock right up against it, and still have alignment and shifting problems.

Frankly, I'm amazed that the shop didn't fix it for you on the spot. Not difficult, wouldn't take much time. Telling you how to do it but then leaving you on your own - well, I suppose if they're swamped, but they would have gained a great deal of goodwill by showing you how to do it and then doing it the first time for you.