I think you are only confusing yourself by trying to shoehorn current library file formats and standards into poses created with legacy content creation utilities.

First of all, material files are NOT "MAT Poses." They are library-specific files that store material setting information. 

The other part of your problem is that you are using OLDER TOOLS to create binary morphs and injection/remove files. Bear in mind that some of these tools were created years ago, and as good as they were back then (and yes, I am indeed a Dimension 3D fan), they are not aware of newer file formats and parameters. In the case of Dimension 3D tools, I'm certain that they do a syntax check before saving the files, which explains why some settings are changed during saving.

In addition, the Pose category has become a catch all for all sorts of different files, and it's gotten so unruly to keep track of what is what. There are character poses (which the library category was originally created for). Then you have morph injection and remove poses. And then there are material poses. Looking at my V4 runtime, the Pose category goes on forever, and because of the naming it's like hunting for needles in a haystack to figure out which type of pose it is. 

Old habits die hard. I know. But you might be making things more difficult for yourself, and for users, by trying to do things "the old way."