If the labels don't carry enough information to be unambiguous, then they are effectively unlabeled.

The programmers who assumed x, y (lon, lat) were coming at the problem from the wrong culture; the geographers quite correctly clarified things by labeling data with the usage from their cultural perspective. One thing that I've learned over the last few decades is that if a specification is ambiguous, then it's my job as a programmer to ASK THE CUSTOMER how to resolve the ambiguities and not just figure that I know how it should be. I have a nasty habit of including the software version taht wrote a particular file (as well as applicable spec versions) so that I can deal with errors like this later.

Geographers are related to navigators in much the same way that mathematicians are related to physicists (the one is a theoretical underpinning for the works of the other). Navigators have a historical perspective where they can determine latitude unambigously by angle of the sun above the horizon and time of year, while longitude was much more difficult to determine, and they were rarely much above sea level. From that perspective, latitude would come first in the coordinates, longitude next, and altitude (if anyone cared at all) dead last.