They should be pretty interchangeable, with the position in weapons.tbl just defining where they show up rather than how. Also, any weapon should be usable as a countermeasure - I don't know why the wiki says it has to have the countermeasure flag. When I did the initial testing I was using Subachs, and that would be a stupid restriction to put on it in any case.
Anyway, you should be able to make primaries that use the POF renderer and secondaries that use the laser renderer, and stick primaries or secondaries on the countermeasures slot of a ship, or make missiles that are also countermeasures. (Or primaries that are also countermeasures?) But mostly they should be more interchangeable than you think, and more rewarding to experiment with.
This isn't anything new but there was a bug that I fixed almost a month ago that prevented this from working properly. This interchangeableness is intended, though. If something isn't already possible then the majority of the code required should already be implemented.