@k_b : No, not specifically BWV131 (“Aus der Tiefe”), but it could have been…
When (or if, these days) we perform 17th or 18th Century music with historical instruments, we often tune to the so-called Chorton-pitch - a common pitch for organs at the time - of approx. 465 Hz, a semitone above our modern 440 (the string instruments may use slightly thinner strings, but access to suitably tuned keyboard instruments is sometimes practically difficult). So we sometimes have to be “bitonal”, which means using keyboards tuned to Kammerton (a - 415 Hz, semitone below modern pitch), and transposing up. And the lutes are complaining, too…
So we need transposed scores, and luckily - thanks to the ingenious foresight built into the very concept of Dorico - this is not usually difficult to achieve. It was a slightly exotic situation which triggered my OP above.
However, your mention of BWV 131 reminded me that such simultaneous use of two different pitches was a constant feature of Bach’s own performances throughout his life. Based on two different principles:
In his early years (Mühlhausen, Arnstadt, Weimar) the strings and brass tuned to the (high) organ pitch, but the Kammerton-tuned woodwinds couldn’t, so they had to transpose. BWV 131 is in g minor, but the bassoon part in a minor, and that is the general tendency in Bach’s - and many others’ - output from that time.
And Bach even went one better in the early and wonderful BWV 150, where he wrote for a bassoon in Tief Kammerthon (ca. a - 390 Hz, minor third down from Chorton). So score and strings in b minor, bassoon in d minor!
Bach reversed this principle, when he became Thomaskantor in Leipzig in 1723, and adopted the local practice: All instruments were now in Kammerthon, and the organ transposed., which explains why all the organ parts in his Leipzig church music are a major second lower than the “home key”.
Example: BWV 140 “Wachet auf”, score in Eb, organ part in Db (!), which incidentally shows that at least some organ “continuo” registers, if not the whole instrument, must have been tuned in a circulating (non-mean-tone) temperament.
This also explains why Bach often raised the pitch of his earlier works, when he made repeat performances of them in Leipzig.
Example: BWV 199 “Mein Herze schwimmt in Blut”, Weimar version c minor, Leipzig version d minor. But the actual performing pitch remained constant! And he could still use his original Weimar oboe part…