The OP was in the transition sleeper, since no other sleeper on the Zephyr would require walking through coach cars.
The best suggestion I have is that he should write up a brief description (similar to what was posted here), with details of trip dates and reservation number, and send it to Amtrak customer service.
The key issue that should be corrected is that of the crews speaking loudly, at night, in earshot of other passengers. I know this has been brought up in some customer service classes before, but I couldn't say if it's necessarily been pointed out to all the crews or not.
As for the issue of dinner reservations, it's hard to say. If the sleepers were full/sold out, then somebody's going to wind up with last pick of dinner times, even if they were sitting in their room waiting for the LSA to take reservations. Whether the last to pick (before coaches) happens to be the transition sleeper, or the lower level of the 632 car is just luck of the draw. On multi-night trips, LSAs will often switch up which sleeper gets first choice and which one gets last choice. In this case, the OP implies that he was only there for one meal, so it's hard to say if the LSA would have given that car first dibs for reservations the second time around.