Well, I like roomette 2 and often ride there and usually there is no odor. Often the odors, if any, are limited to downstairs, particularly the H room which is right by the holding tanks.
Sewage odor problems come in a lot of variations, most commonly limited to downstairs, sometimes downstairs and the Bedrooms above the piping on the "wet end" of the Superliner. On some sad occasions, the entire car. The upstairs lav, in and of itself, is usually not a significant source of odor unless it isn't being kept clean. If it is that stinky, the problem lies deeper within the system.
I'd treat it as a one-off. If the odor is getting to 3&4, it is probably everywhere in the car. It's Amtrak, you win some, you lose some. The occasional car that has a sewer smell throughout is part of riding Amtrak. Ride enough, and you'll eventually encouter a stinky car. You'll also eventually eat the "we're 8 or more hours late" stew, have a car where the HVAC is stuck on high A/C, stuck on high heating, or just doesn't work at all. Maybe even have your roomette the door jump its track and jam, requiring a conductor with a crowbar to free you. You can't generally outguess Amtrak's Gods of Fate and the Coach Yard. However, it appears you did not suffer the other issue that often appears associated with a whole car sewer smell, that being the toilets not working at all.
Occasionally, the cars are simply stinky. Not great, and probably yet another source of "never agains" but a sad fact of life onboard Amtrak.
