In transcribing a manuscript it is best practice to transcribe diplomatically exactly what the MS says. 

A second, separate file may be prepared that contains various normalisations, like ba/va or śa/sa, rma/rmma, etc.

To normalise the main transcription file takes away the opportunity to study these phenomena.  And in any case, the majority of these features can be manipulated with regular-expression rules, as in Saktumiva.  So there's no need to normalise them. 

Best,

Dominik