It's a good point about compatibility. I hadn't thought that through; I guess I just assumed Siemens would be making sets of locomotive-hauled coaches with the same trainline, air, HEP, coupler, and diaphragm standards as the existing locomotives and cars, so that it would be easy to just couple an extra coach or two on where and whenever needed.
But, in any case, doesn't it seem like the Horizons and the Amfleet II's will be around a while longer? Might it make sense to assign five, ten, or a couple dozen Amfleet I's to wherever those cars are still operating? Examples:
If the Illinois trains on CN tracks are still going to use Horizons and still have to lug around extra cars for axle count, why not assign five or ten Amfleet I's for axle count instead of using old baggage cars, spare cafe cars, and whatever else comes to hand? Then it would be simple to open up an extra coach when there are a lot of passengers on those trains, and potentially possible to swap in a baggage car or whatever if one of the coaches is needed for a surge on some other route.
The eastern Long Distance trains that apparently will have Amfleet II for a while yet could get an Amfleet I for local passengers at peak times. (But it's completely possible that the economics just don't work out.)