Without getting into the details of why you should or could or would
tune the organ one note low, there is a very easy way to transpose
a scale up or down by any number of notes.  It doesn't matter if the
instrument scale is chromatic or not because you tune each note up by
(for instance) one note, _not_ up to the next note in the scale of the
instrument.

Take a piece of paper that has equally spaced lines.  A piece of
quadrille paper is best but any paper with equally spaced lines will
work.  Draw a line down the center, perpendicular to the printed lines.
Then write the chromatic scale (in order) in a column just to the left
of the line.  Do a couple repetitions of the 12 note octave.  Write
another identical scale just to the right of the line.

You can also type two columns of notes on your computer or one column
and print it out twice, or copy & paste the scale given below into
a text document.  In case you forgot, the notes are:

A
A#
B
C
C#
D
D#
E
F
F#
G
G#
(start over at A again and repeat)

Now cut the paper vertically on the line.  Hold the two papers next to
each other (like they were originally) and the notes on the left are
the same as the notes on the right.  Clever, eh?

Now, slide the right scale up one line.  Now each note on the left
lines up with the note that was originally one note below it.  Reading
left to right, each note on the left now points to a note on the right
that is one note lower.  You can slide the right side up or down as
many notes as you like and the transposed notes will always be correct.

This is especially helpful with non-chromatic scales like in a barrel
organ or a musical box.  The original tuning was often designated by
these familiar notes but with "A" at a completely different frequency
from our modern 440 pitch.

Regards
Craig Smith