datchew, could you be confusing the filter element with the term cannister? That happened to me for a while.
As others mentioned, the length of the filter element isn't the issue with the o-ring, but the cylindrical insert inside the filter cavity.
When I first got my airhead late last year, I read all I could on the subject and still confused the term cannister with the oil filter element itself. I finally understood the cannister was the round cylinder pressed into the crankcase. And when I measured it at 3.1 - 3.2mm deep, I was happy.
I'm with Anton on not being comfortable with using the shim to seal against the metal surface. When I went through my bike, the cannister measured OK, but the previous oil changer had used one shim between the cover and the o-ring, and the paper gasket under the cover. This had the o-ring bearing directly on the edge of the cannister which made a nice even indent in the 0-ring, so I knew it had been reasonably well sealed. But just about everything I'd read says to put the shim in first against the cannister, then o-ring and then cover, sans gasket, unless the cannister depth is less than 3mm. And that all makes sense to me, except for the concern about trusting a metal shim to seal on the end of the cannister. On the other hand, after looking at the groove in the o-ring I removed, I can see real potential for the o-ring getting sliced during assembly if it shifts the least bit.
One of those damned if you do, damned if you don't situations.
Merritt Island, FL
When a person asks you for advice, they don't want advice. They want corroboration.