To further clarify, JPATS (ConAir) planes do not actually have shackles and chains, as some movies have shown. The leg shackles and body chains are put on prisoners before entering the aircraft, prisoners are not chained into their seats. Persons being deported are handcuffed prior to boarding on the planes used to return them to their countries as well, but are not transported by the USMS planes.
If we want to get to playing the guessing game,
now that the US Military has been deployed to protect the borders, they could pack them into a C17 and use that. It is better situated for shackles and chains as you suggest.