This is a reasonable accommodation. All the ADA requires is a reasonable accommodation.
You're saying that like Amtrak has no ability or agency to control modifications at the stations and platforms they stop at. I don't think this is the case.
Further, the height of platforms has nothing to do with whether or not bi-level cars are feasible or desirable. They are not. Stations have bridge plates for boarding off the platform and they go up and down. Even if you aren't in a wheelchair, there are a host of difficulties presented by a full set of narrow or steep stairs that are not presented by aisles across a wide range of disabilities.
The capacity issue you're talking about is theoretical and can be fixed by adding cars. The capacity issue we're facing is that we don't have enough rail cars available. The replacement bi-level for the Superliner failed safety tests and was abandoned. In the time it takes to reboot a bi-level car program, you've lost the ability to serve entire routes.
First off, the longest domestic flight in CONUS is 6 hours 40 minutes. It isn't until you get to Hawaii that you have a 9 hour flight.
Airlines have attendants that are trained on how to make that bathroom work that are on every flight that are available to assist in that situation. They have to be there because wheelchair-bound passengers almost always need to be buckled into a regular airline seat for safety purposes.
Amtrak can't have an attendant on call and has the ability to allow wheelchair passengers to safely ride in their chairs. Given that circumstance, a self-service bathroom is the ADA option. Also, it doesn't cost that much extra to make space on a rail car for an ADA bathroom when you're ordering new equipment. I don't even believe airlines have that as a logical design option on aircraft,
They were cancelled because they couldn't be built to the same safety standards that apply to single-level trains.
So which one is it? There's going to be no electrification or you simply change the electrification standard because you want to have a bi-level train that's less safe, is restricted to serving a portion of the country, less accessible all in the name of...higher passenger density?