What about a checkbox in "preferences" window?
PMF is in most cases useless to me, since it doesn't allow testing anything in game. When I edit a POF, I adjust whatever I want and save to POF to test to see if it gave the desired effect. The only time I used it was when backing up glowpoints for an unrealiable model to prevent loss of my work in case of a crash during saving.
Since I see no reason to use PCS2 other than add data used in game by FS2 (it's meant to do just that, afterall), I don't know why to use it to save anything to a format which can't be opened neither by modelling programs, nor by FS2.
PCS2 is a special case, since it's a program used to put models into game. Photoshop is a program used for creating 2D images in general, so it's own format is the best one, since images can be viewed regardless of their format, and being viewed is their primary purpose. The primary purpose of the models created by PCS2 is for them to be used in FS, POF format is needed for them.