The problem with organ pipes as evidence for old tunings is that they have been around for many years, during which time organ maintainers have, shall we say, buggered about with them a good deal. If a pipe is, to the ear of the tuner of 1802 or 1777 or 1913, a bit off, he can crop a bit off the top to sharpen it, or close it up a bit (just a bit) to flatten it... on top of the original variability of pitch and temperament, there is the taste and fashion of subsequent generations, in the case of old organs lots of them. It's a bit like old English churches, the Victorians were only the most notorious of a bunch of vandals happy to hack at window and wall to make it suit their taste.

bluesunsets- I'm sure your teacher was a brilliant musician, but what a wonderful excuse for not always hitting the note the hearer expects. With tone holes the player can bend the note (I'm not by any means good, but I can blow a quarter tone sharp or flat), and adapt to what he hears.