[Micheal Espinola]

Almost 10 years later, but here is your answer – if you never found out on your own:

One is a raw stream, and the other is not. Streams are saved in small bits (.mts files) that do not have “start codes” indicating where they stop and end. When you save (concatenate/recombine) a stream to a proper file, the start codes are added.

The codec is the same, but the formalities of the file internally have different indicators.