Well thanks Gabel and Derek for what I would call I believe very educated answers.
First part-- Gabel--pretty good response I would say--
The original framer when he laid out for the mortise to secure the bottom of the purlin posts had it in his mind that the exact centre of the rafter would bear directly on the outside corner of the purlin plate, and that necessitated moving the mortise over 4" closer to the centre of the building the posts being 8" square. In my book this was pretty good work and it certainly was not done by a green horn, but by a very experienced framer who was pretty particular I must say.
I had sort of forgot about it until we were doing an initial layout of a pair of rafters on the ground prior to the raising and discovered why the mortise ended up where it was.
Derek:--also a good guess I must say
The extra height over the walkway gave a little more clearance for the horses heads especially their ears as they entered on their way to their stalls.
Personaly I would have put the ceiling timbers in level if I had been the one in charge of the framing at that time.
I must say though that lighting was not a factor because of the small windows in this case.