The operating word is "reasonable". This was from the Dept of Justice page on the revised ADA guidelines:
Entities covered by the ADA must modify their policies to permit miniature horses where reasonable. The regulations set out four assessment factors to assist entities in determining whether miniature horses can be accommodated in their facility. The assessment factors are (1) whether the miniature horse is housebroken; (2) whether the miniature horse is under the owner’s control; (3) whether the facility can accommodate the miniature horse’s type, size, and weight; and (4) whether the miniature horse’s presence will not compromise legitimate safety requirements necessary for safe operation of the facility.
There can't be any forcing of removal of seats, as that's not something practical to do on short notice. There are reasonable ways to accommodate a service animal that will not be considered isolation or segregation. If the animal can fit in front of a seat (like many service dogs) that's fine. If it can only be on the upper level in the aisle that's not good. If it can manage it's way upstairs, then maybe an end seat would work, as there's lots of legroom. There's got to be a certain standard of reasonableness.
To me, and to any objective person, it is reasonable for Amtrak to comply with the Justice Dept and accommodate a miniature horse, when the miniature horse meets those listed requirements.
I guess, I don't see
six years (from 2010) as being "short notice", as you seem to feel. Amtrak had those six years to make what ever modifications are required. As I suggested, if they need to allocate floor space for a service animal, one way to do it, is to remove a seat or two.
This is similar to the need to create space to accommodate a wheel chair. Your reasoning is that someone in a wheel chair must be able to squeeze in, between the cushion of one seat and the back of the one in front of it, because they don't deserve any modifications.
BTW, a member of our family is in a wheel chair. When she accompanies us to baseball game, we simply call the stadium in the afternoon, and they remove three seats out on the suite's balcony, to make a space for the wheel chair. So, others can do it.