However - he mentioned that the feedback from crews is dramatically different, and he said Amtrak really took that into consideration... that the crews can not get disabled folks up and down the stairs, smokers can hide out in lower levels, open windows, etc, etc.. The crews prefer the ease of walking car to car with no hidden levels and they like having everything in clear view. There is tremendous liability in keeping the train safe and secure....The Superliners are just harder on the crews...
All that is true, but the future bi-level cars for LD trains need not be a clone of the present Superliners. Many of the issues you describe can be fixed. Windows can be locked. Doors can be interlocked. Even a wheelchair elevator is not beyond the realm of the possible.
On the other hand, it all boils down to the economics. Single level cars means that trains will have to be longer to provide the same capacity. Will all stations be able to handle that? Will locomotives need more power to pull the extra weight? A lower level of car will of course lose some of the viewability experience from the present Superliner lounge cars. Maybe somebody con bring back some version of the dome to make up for that.
At the end of the day, myriad reasons will influence the decision, and it will be difficult to second guess the outcome so many years in advance.