I seem to remember that on the KSSU DC10's the EPR was measure between the pitot probe and the 5.4 station, there was no Pt2 probe. So it wasn't a 'real' EPR anyway.
I believe it was mostly used for condition monitoring. As the 5.4 pressure still is on some ships.
You are right about the -40. Dunno why anybody would choose the JT9-59A over the -50C. Sure it is more solid, but then it also needs to be. And it needs a lot more 'fixes' for airflow control in the compressor.