I do not think that it matters whether the weather seal is attached to the cover or the coaming lip.  With the hatch lid in place, the weather seal will be compressed, preventing water from entering the compartment so if exposed to constant water that gap will be wet either way.  Generally speaking, I do not think that water there is much of an issue because most boats are stored inside and have ample time to dry anyways.  For a boat stored outside, it would be best upside down.

On a related subject, I will tell you that with the flush hatches, it is VERY important to make sure that the end grain of the plywood deck is thoroughly sealed with epoxy.  The Shearwater Double was my first build with flush hatches and I thought that I had sealed the end grain.  The boat lived in the garage for a couple of years then we took it on a week long vacation where it sat on the trailer and it rained every day.  A few days later, I noticed some discoloration in the deck around the hatches in areas that I had not sufficiently sealed.  

   I've done invisible hatches on both my kayaks.  I think the concern about water retention based on whether the gasket is glued to the rim or the hatch lid is minor.  I selected putting it on the rim, because that meant the water had to go "up-and-over" (instead of just sneaking under) the gasket itself to actually get into the boat.  That concern for a well-selaed gasket is also probably minor.  I thought about attaching the gasket to the lid not based on the concern you describe, but to protect it from and nicks or gouges or whatever putting things in and out of the hull - but didn't do it based on my "up-and-over" consideration.  Even so, I've never damaged the gasket material while loading the boat.

One more thought - storing the boat upside down is a good option - and in that case unless you're worried about animals getting in the hull having the hatch covers totally off/open might be a good option.  I usually store my kayaks upright either under a waterproof tarp (when outside) or in the garage.  But in every casue, up or down, covered or not (and even conventional hold-down tabs or invisible hatch shock cord hold down) I advocate for unlatching/loosening the hatch so the hole is open or the hatch cover is just resting in place.  All to protect the resiliency and springiness of the gasket material - so that it is only compressed when I'm actually using the boat. Also in the case of invisible hold down to lengthen the life of the hold down bungee.  Even these concerns of gasket and hold down bungee resilience might be minor, but I think it makes for a longer gasket/bungee life and better seal when the hatch is in place. 

Thaks, both, for your comments.

Mark, you have a magnificent fleet there!