They're reverse engineering the program from its effects (the files it reads and writes). It's not possible to exactly duplicate the original program's source c

They're reverse engineering the program from its effects (the files it reads and writes). It's not possible to exactly duplicate the original program's source code in that manner, nor is it necessary. When there are two indistinguishable approaches—in this case representing something as a message in the .proto vs representing it as bytes and later decoding it separately as a message—it makes more sense to choose the simpler way.