The job of a good transcriber is to render the document as faithfully as they can. This includes transcribing words as they are spelled, not changing obvious errors, and not adding material that is not there.
Notations, if necessary, can be made separately and an analysis of the perceived accuracy can be done separately as well in a way that makes it clear where the document ends and the analysis begins. But a transcriber’s job as a proofreader should only go so far as to make certain she has rendered the original document as accurately as she can, warts and all.
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And if at all possible, include a scan of the original document on the page opposite the transcription.