I agree with you 100%, It is the design of the hatch itself that is very very bad.
I own a very successful product design engineering firm (my day job), and my hobby is kayaking and sailing, so my interest here is only because it's fun for me, I have no connection with Hobiecat company at all.
And to be fair I can look at pretty much any design of any product and giggle at why in the heck did they do this or that, so I'm not knocking Hobie in particular here, as a whole they are better than most.
However the design of the hatch seals on all of their hatches on all of their kayaks (including the AI/TI) makes me laugh (LOL, or LMAO), as they have been making the same mistake for many years over and over again, shooting themselves in the foot again and again with every fix/improvement they make to the hatch design on all their boats. They are forcing themselves to try and manufacture a product to un-realistic tolerances when there is no reason neccessary (driving cost up ("which affects me")).
The simple fix I discribed earlier should help on your hatch cover also, at least until Hobie fixes your boat (which they should do). I made a picture showing why below (the underlying engineering).
In picture 1, this is showing the current design as it's supposed to work with two compression/butt (static) seals pressing against a flat surface. This type of seal is fine on something that you know is going to be flat everytime and doesn't move (like a canning jar lid), and can be easily manufactured to high precision. As an example a 1 gallon paint can lid uses two pinch type dynamic seals to seal the paint can, because a static compression seal would not work, and would be un-realistic to manufacture.
The hatch seal Hobie has can probably withstand a variation in flatness over the entire surface, ie.... flatness of both the hull and the hull lip being maintained within a manufacturing tolerance of around 1/16 of an inch (as long as it doesn't move). This also requires that the lid be manufactured to similar tolerances. To be honest, this is un-realistic in any type of plastics (especially rotomolding). Even auto manufacturers using stamped metal on door seals cannot hold these kind of tolerances.
Pic 2 shows the problem you are having, with a gap in the center, allowing water to flow freely into the hull.
Pic 3 shows the addition of a simple piece of tubing around the hatch, this adds the type of seal that should have been used in the first place ( a pinch type dynamic seal).
Pic 4 show that even if the hull is bent, or the cover is ill fitting, or the hull flexes (which it does in the waves) the water seal is maintained.
Basically you cannot use a static compression seal on something like this (engineering 101), please refer to any seal design guide.
Hobies hatch design is not my problem, I only came up with a simple fix to help my friend Jim so he can stay dry next week doing the EC challenge, and I'm not about to tell Hobie how to design their boats, but I do like to use them.