We do get the same effect as the real CSM and LM, but probably more accidentally than simulating something in a super realistic way. The CO2 from the astronauts accumulates in the LM over the course of the translunar coast, where it doesn't get scrubbed as the LM is unpowered. I think it tends to go to some manifold in the suit circuit. So once you activate the LM ECS (I think it's the step where you start the suit fans) the CO2 will be evenly spread over the suit loop, including where the CO2 sensor sits and is now being measured as very high.
With the LM ECS fully running this problem does go away after a while, although for a bit it's probably unsafe for the astronauts. A quite recent feature, and a bit experimental still, is on the ECS page of the PAMFD. There is now an option to install a hose connected to the CSM suit loop through the tunnel going into the LM, creating a slight overpressure and leading to much better air circulation. So that's a realistic solution to a realistic problem and it seems to work quite well in NASSP. But you would have to do it for many hours to have a real effect. With the suit fans running the CO2 scrubbers in the LM will also eventually do the job, just takes a bit.
The
LM AOH Volume 2 has the procedure for the clock synchronization, "LGC/CMC Clock Synchronization Routine (R33)". Routine 33 it refers to is simply doing V06 N65 to show the AGC clock time.
For the TEPHEM, that is the precise liftoff time in triple precision, so three octal numbers. And you want to use this as the time reference for mission elapsed time in both CMC and LGC. So the procedure is to simply read out the numbers from the CMC and then input them in the LGC, so that they are the same in both computers. So the V05 N01E, 1706E just reads the numbers from the CMC. And the V25 N01E, 1706E is used to enter the three numbers into the LM DSKY. A V05 N01E, 1706E is then the check that the numbers were correctly entered into the LGC.
Clock sync is slightly more involved. As you can't be two astronauts at once in NASSP, pressing buttons on two separate DSKYs at the same time, we have a button in the PAMFD, LGC page, to do that. So you type in V06 N65 on both the DSKY in the CSM and LM. And the "ENT" button on the LGC page of the PAMFD is then pressing the ENTR key on both DSKYs at the same time for you, showing the clock time of both AGCs at the same time, too. What you would get there is e.g.
LM:
+00100
+00000
+00000
CSM:
+00100
+00000
+00012
So that would be 100:00:00.00 GET in the LGC, 100:00:00.12 GET in the CMC. A clock difference of 0.12 seconds. So you need to increase the clock time of the LGC by that same 0.12 seconds. And that is what Verb 55 is for. You would enter:
V55E
+00000E
+00000E
+00012E
To increase the clock by 0.12 seconds. And when you then repeat the V06 N65 procedure with the PAMFD ENTR press you can then see that you have the clocks synchronized.