There are so many variables. It sounds as if you are a concientious craftsman and attempt to perform your work perfectly, although wood and humans are rarely perfect.
A gap is difficult to live with, but it can become a reality if the material shrinks excessively, etc.
I personally do not employ the post to rafter connection, but I could imagine the post shrinking away a good bit.
My experience with looking through Timber Homes Illistrated is quite the opposite of yours. I find gaps, poorly executed joinery, etc all the time.
I personaly would have to find out why the gap occured and take steps to remedy it in the future.
I dont know if it is true but I have heard that when a Japanese Tea House carpenter makes a mistake, they leave it. It represents the days work. No more/no less.
