Amtrak seems to be generally bike-friendly, and I take Basil on board without any problems, and with no disguise.
If I wanted to, though, I could bring my Brompton aboard as carry-on luggage: He’s nearly half the weight limit of 50 pounds, and, as you see, fits nicely into the carry-on verification schematic, even though the seat post isn’t fully dropped in this photo. I might pop him into a bag if going the carry-on route, though, just to avoid any questions.
(Basil’s under-seat bag tucks right next to the frame when compressed. It’s not going to cause any carry-on issues, even though it’s technically over the line here.)