It is intuitively clear that the header is something that is at the start of the buffer and the footer is at the end. But I am confused how the buffer is filled with intermediate data. Based off the AN75779 I understand that 16kB buffer is built as the 12 byte header, 16,368 byte data, and 4 byte footer (this is explicitly said in section 5.6). Now, going to the state machine design, we have counters that are initialized to count from 0 to 16,367 (as said in section 3.6.3 step 6). I am missing the connection how "Something" knows that the buffer must be filled with the data not from the beginning, but starting from the 13th byte address? In other words, why is the counter set to count from 0 to 16, 367 and not from 13 to 16,380?
In addition, why don't we fill the remaining 4 bytes with the data? I know it is not a lot to waste, compared to a 16kB, but what are the complications?