You all gave me a lot to think about. I've been playing for 3 weeks now. I've tried 4 or 5 approaches. I got some to work, but they were rather clunky. Some of them did not work at all.

Then one day while browsing through the Poser official documentation, looking for some info on how the Shader Nodes hung together, I ran across a note that said that there was a way to call a Python script from a .pz2 file. Since an .mc6 file has a similar structure, I tried it there, and it worked!

So now I have written a script and stashed away in my primary Runtime, and I can hack an .mc6 file to call it. It then changes the Transparency map without changing the Texture map-- or vice versa, depending on what I put in the hacked .mc6 file. The neat thing is that the hacked file appears in the Poser library, just like all the regular material files. And it behaves the same way, too-- if you click the double arrows, or double click on the file, it applies the Texture or the Transparency (but not both). So it feels very much like standard Poser.

It turns out that the hacked .mc6 file can be very small-- only about 15 lines, most of which are just curly brackets. It would be quite possible to construct the files in a text editor. However, my keyboard skills consist mostly of creating typos, so I wrote some other Python scripts to build the hacked files. They work as close as I could make them  to working like clicking the + button at the bottom of the library window. I stored them so that they show up in the Scripts > MaterialMods  menu. 

I've got it all working on Poser 12 on my Mac. If there is the kind of interest that Nerd mentioned, it might be interesting to see if the scripts work on Windows, and maybe some other versions of Poser (Poser 12 uses Python 3, while I believe earlier versions of Poser used Python 2; so there may be some issues with that.)