I did flush fitting hatches with an invisible hold-down system on my Chess 17.  I didn't cut the hatches in until after the deck was finished, including being glassed over.  I then used the cut-out as the hatch lid.  The lid did spring flatter after being cut out, then had to be bent back to shape as the strongbacks were glued on. I cut "hooks" into the center strongback as the attachment point for my hold down bungee system.  (If I remember correctly the smaller hatch only had two strongbacks, so I added a center strongback to keep the pull-down force evenly distributed on the hatch.)  I developed my own sort of under hatch rims out of the kit parts, and carefully selected the gasket material for best seal.  Of course this is all a little extra work, but worked out well.  The most important thing to note is getting the curvature correct - every build is probably slightly different, and small differences will be noticeable - the curvature of the strongbacks might need to be slightly adjusted to match your deck.

Perhaps much easier to describe with pictures than words.  To avoid all the forum posting problems ff you text me at two one zero 846 809six I'll send you some pictures.

And as a final note, from some pictures I've seen of CLC and other manufacturer's kayaks, if you go for the flush hatch WITHOUT doing invisible hold-down, you might need to add some "ridge pieces" on the top side of the hatch so that the hold-down straps get lifted up off the deck and thus develop downward pressure on the hatch.

I went with the standard hatches on the two Chesapeakes that I built but it would be easy enough to go with flush hatches instead.  You can do it yourself like Bubblehead describes above, but a much easier approach would be to order the Flush Hatch Kit from CLC.  It has everything that you will need including a lid doubler so that the lid holds the proper shape and does not flatten as described by BH.  The kit comes with wood toggles to hold the lid on.  If you would rather, you can buy Delrin toggles from CLC or they also carry an Invisible Hold Down Kit.

I have used that kit in four strip builds.  The obvious plus for flush hatches is appearance.  The negatives are that because of the sill, the opening into the storage compartments will be a bit smaller.  This may be an issue if you plan to carry a larger tent or sleeping bag.  The other con is that flush hatches are a bit harder to make watertight than the standard Ches hatches.