AFAIK the radar transponder isn't simulated yet. At least I flew 11 some time ago with the transponder (accidentally) switched off, but the LM radar still tracked the CSM. Same goes for the VHF ranging in the CSM: it doesn't look if the LM is configured right.
Radar transponder is indeed not implemented yet. VHF Ranging is implemented (for Apollo 10+) and it does actually need the right switch configuration and systems powered up in CSM and LM. It only doesn't check if the antenna is in the right position to receive a signal. It only checks on min and max distance to the LM.
The CSM High Gain and the LM Steerable Antenna are implemented, but have no auto tracking yet. For the CSM that is currently being worked on and should be ready soon.
So just to laymen it, for the S-band on the LM It's working as long as V06N51 is showing "tracking"?
Also in 10 it seems the MCC is about 40 mins behind the checklist times, I somewhat recall reading some issue about the time accel being the cause of this? It that right or did I swiss-cheese my research. Anything I can do to fix mid flight?
40 minutes is pretty high, I've not seen more than 25 minutes on my tests. . As for the other time difference, it's probably something with the TLI targeting parameters for Apollo 10 we use. If it is something fixable in the TLI targeting then we will get 15 minutes back at least once it is fixed.