Do you mean store MAT files in a different folder from normal pose files? If so the answer is yes. Normally any pz2 (pose) file under the Pose folder can live in any other folder that is a under the Pose folder. As long as the pz2 is somewhere under the Pose folder it should work. Theoretically you could get a situation where a pz2 in a pose folder calls another pz2 in a pose folder via a 'readScript' statement. In that situation moving the 'called' pz2 would mess things up, but I have never come across such a situation, so I think you are pretty safe moving anything under the Pose folder.

pz2 files that live outside the Pose folder (eg in libraries/!DAZ) are a different matter, and you should not move these files.

So you could, for example, have a folder structure like this if you want:

Runtime
        libraries
                Pose
                        Figure Poses
                                P4 Poses
                                Jessi Poses
                                V3 Poses
                                V4 Poses
                        MAT Poses
                                P4 MATs
                                Jessi MATs
                                V3 MATs
                                V4 MATs
                        Utility Poses
                                P4 Utils
                                V4 Utils

I'm not recommending the above structure, I only give it as an example of what you could do. You can also move pose files under the camera folder providing you change their file extension to cm2 (or cmz for compressed p2z files).

Or have I misunderstood the question?