Here's a little issue we run into now and then. Which reference designator goes with which part? Quick. I need to know. Now. Now. Now!
It's less of an issue with SMT parts because we machine place them and use your centroid file to do the programming. Still though, It's always good to have things marked clearly in case rework is needed and for visual inspection.
For thru-hole, though, it is definitely an issue because a real human being is putting the parts in and the visual markings are the programming for the human type person.
For best results, take a little extra time and make sure all of your ref designators are clearly associated with the correct part. It's also always a good idea, when possible, to have all the designators in the same position relative to their part. Consistency is a good thing here. Consistency is a good thing with mashed potatoes too. Who likes lumpy mashed potatoes?
You say poe-ta-toe, I say ugly brown tuber