As you say, in M81 NBA has F# eight note followed by G quarter note in the pedal while most other editions, including the 2012 Breitkopf (ed Zehnder), have G quarter note followed by eighth rest.
Neither is obviously better so either is fine. Bach may well have played it both ways at different times.
Long story short, there are several sources but no autograph. The "blue note" version appears in only one of them: a Johann Tobias Krebs manuscript with an incomplete pedal part. This may be an early version.
If you want to read the details Breitkopf provide their English language commentary for free download on their site. https://www.breitkopf.com/assets/pdf/15014_EB8804_PDF_EB8804_com.pdf
- Adrian.