I would just carry the same line thru both, or even level off the blue sill to make a shelf (if the water gets that far then "we" have a bigger problem). If the blue is a counter space the flatter surface would be far more useful. If there is something going on inside that dictates the vertical height under the blue be higher, if it is a foot well for the mattress and the extra height is needed inside (under the counter, as it were), then I would raise the lower edge of the hatch up to suit. On the other hand, if it is a storage well, then I would shorten up the inside (move the forward edge of the blue sill back) so that it is less of a reach to lift things up over and out.
I haven't read back thru the thread (and my memory is not so good), but I am assuming you intend to use some sort of weather seal (although I vaguely remember some talk somewhere about designing a hatch with no seal).
Again, you may have a bigger design picture in mind than what I am looking at here, so my comments might be off. Take it for what it is worth ($0.02).