Yeah, those are not going to work right. The S-IVB for example has really low thrust thrusters, so it would work about as well as the autopilot modes with the ISS in Orbiter. And the last remnants of it for the CSM and LM have been removed after the NASSP 7.0 release. So maybe they are still working in that release version. I never checked.
Starting with Apollo 15 the CMC actually got a whole suite of tools for pointing, useful for PTC and pointing the SIM Bay at the Moon. So with Apollo 15+ you can use Program 20 of the AGC to do exactly the same things as the Orbiter autopilots.