Here's another compatibility problem due to PDN (3.36) not saving out color values on pixels where the alpha value is zero. I think this information is new to this board and worth your consideration, but I understand that you've discussed the issue before, and I'm not asking you to debate it further.
The incompatibility is with Civilization 4. It requires its file "GameFonts.tga" to have certain pixels with zero alpha and certain color values. (It doesn't render those pixels; it uses the color information in them for something else.) So I can't edit the file with PDN. I have to use Gimp instead.
I figure if we report enough incompatibilities, you might eventually change your mind for reasons of practicality.
A related argument in favor of changing PDN is that TGA 2.0 allows files to "abuse" the alpha channel. Granted, the place where the file specifies what it's doing with the alpha channel is [field 24 of] the Extension Area, the interpretation of which is stated to be optional. Still, there is support in the spec for the point of view that alpha need not always be interpreted strictly for rendering.