Genealogical documents present transcription challenges, especially the older they are. One wants to make it clear in any typed up rendering of a document what comes from that document and what comes from the researcher’s mind (or other sources). I have a simple approach that I use when transcribing any document. The transcription is clearly indicated as such and put between two markers in brackets indicating where the transcription begins and ends. The analysis or commentary is after the transcription.
That helps me to know what the document said and what I thought it said.