I have looked at this from several points of view, to try to get into the guts of it. No luck so far.
Document > LayerStack Property > LayerObjects Collection > LayerProperties Property > LayerProperties Object. All the properties are read-only
Document > SetupParameter Property. Nothing about stackup in in there.
Undocumented functionality - there are a number of ces-related dll's and executables in the Mentor install tree. I've looked at some of them, but so far nothing fruitful.
CES has its own process but the Stackup Editor apparently does not. There are brute-force methods of affecting the actual application windows by way of automation, but doing it this way is not really the way to go.
If you do find anything I'd be very interested to know of it.
We have the same problem, no solution yet…
We currently try to find another problem related with the Drawing Editor and the Stackup. We have a Function in our Automation ”Create and Open Master Drawing”, this function is not working properly on 2 Layer Designs, if you change the Layers to 4 it will work without problems. Something there together with the Automation seems to not work right.