You should download the pmw133.zip file from that site, extract it's contents and then use PMWBIND.EXE on the apocalypse exe's. Easiest way would be to unzip pmw133.zip to it's own folder and copy UFO2P.EXE (cityscape) and TACP.EXE (battlescape) to this folder. Then you open a cmd window, navigate to this directory and type "PMWBIND.EXE /U TACP.EXE". This should create a file called TACP.LE I think, which you can then open using IDA.
I'll take a look at the apatcher source code to see if I made a mistake, thanks for the report The intended behavior is that Y enables it, N disables it, and A (abort) leaves it as it was.