The reason is that the radiated wave directions emanate out through the laminations direction and not from the bell pri and sec sides. This is especially true if you mount your power tube(s) near the end of the laminates as they'll get affected by this. My disclaimer is that not all grannies are the same or react the same and why it's such a good idea to do this little part before you build if you can.
I have not tried mounting a PT in different ways to hear the difference but...
I seem to remember a post not to long ago here on this subject, ie; core orientation and noise. IIRC, Z mounting of the PT was said to have the least noise. Yes I realize that's not the issue here but again IIRC, a pic. was posted from Merlins site showing and saying that most of the EMF radiates from the -- corners -- of the laminations, which struck me as odd. I had never heard that before, not that I know much about it. Then IIRC someone, (HBP's?) brought up something about the core windings in a EI PT can be wound in a different orientation from another EI PT. Which I still don't understand, not saying it's not true.
Now jojokeo relates his tests to show the most EMF waves radiate out through laminations.... which I take as not the corners but 90 degrees from the end bells.
Now in TUT 3, 4-12, KOC writes, "most magnetic leakage radiates from the end-bell face" 90 degrees from the laminations. Now a lot of guys there have built a lot of amps according to this placement of the PT core and are very happy.
Now I don't profess to know which is best from experience, but I do have a question.

If most of the EMF waves radiate from the laminations, be it from the corners -- or -- off/from the flat ends, then why would any one bother to use end bell shields --- and/or --- copper flux bands as EMF shielding?
The price of the PT (or OT, choke) would go up and the "bean counters" would never go for that if it didn't make a difference. At a certain point in production Leo switched over to using all shielded PT's, OT's and chokes. Even Fenders Z mount PT's had end bells after a certain point in production.
Leo was a good businessman, if all he had to do was turn the core 90 degrees. why would he spend the extra money on end bells?
Marshall used them after a certain point also.
Thanks, Brad