The programmer doesn't normally care about the endianness of the file to be programmed. It just wants the file to have the bytes to be programmed in the order they are to appear in memory. The endianness of the file is set by the compiler/linker.
The only time the programmer would care, is if it needs to separately update a field in the file such as the version number. Only then does it need to know if that data is big or little endian.