My current understanding is that both the manuals and the pedal keyboard of the Organ play at concert pitch unless the composer requests a stop which transposes the pitch.

However, I listened to a recording of Koopman playing Bach's Passacaglia and Fugue in C minor. The pedal part sounds abnormally heavy for the pitches indicated in the score, my guess is that Koopman was using both the standard 8 foot stop and the 16 foot stop to make the sound thicker. Is this common practice? I generally associate the pedal keyboard with a heavy contra bass sound, which doesn't fit with it sounding in the register of a regular bass instrument, so I assume that use of 16 foot stops isn't unusual.
You have the sheet music? Organ music typically has three staffs. Are you looking at a piano version that doesn't have a pedal staff?

You can transpose in octaves, yes, some stops are available on the pedalboard and the manuals, but the pedalboard is for bass notes. Each pipe organ is different and has a different stop list and amount of stops, so yes it is going to sound different. What makes you think that a 16' is unusual? An organist uses the whole instrument. Question doesn't really make sense.
Last edited by bigblockelectra at Sep 20, 2013,
Organists to a lot of weird things with registration. It's certainly possible to pair the pipes that pedal is controlling to have both 8' and 16' sounding at the same time, which would be really thick and heavy.