It drives me nuts when it doesn't matter. Once I get good tooth grooves in, it doesn't matter as I know which way I like it. I really want a defined top and bottom, for no good reason at all.
What about cases where the stem is flush/even with the shank? Aren't the pipes constructed/sanded with the stems in a given direction so that they'd line up perfectly?
Just got my response from the maker: "Normally there is one position where the stem and shank meet smoothly since I hand fit them. If on your pipes they fit either way, I am surprised. Just a matter of luck more than my skill."