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Follow up...
I pulled out the new seal and laid it up on the bow. I found that my new seal lays up better with the long flap on the outside which matches how my original was installed. I think it's more to do with the shape of the seal than 'flap length'.
The seal isn't uniform in its construction.
The 'long flap' side has a thicker base between the channel and the hollow 'tube' of the seal.
In the photo above you can see the indentation left from the clip from the stainless trim (outside).
In the photo above you can see the indentation left from the flat black metal trim strip which runs along the interior of the top and the seal.
