Stern and especially bow lines are required – so no cantilevering, and rack stresses by side wind loads are minimized by being taken by the end lines. Boat is carried right side up [it’s rockered curvaceous shape is supported adequately by the rack spacing – think of the diffential loading in abrupt changing conditions on and in waves when we’re paddling!]. As Peter mentions, main heavy loading is in the centre with the sprayskirt attached and the waist opening tied off and inverted [or a ckpt cover if present] to eliminate rain ingress at speed and use the end compartments for the light items like clothing, tents etc.
For the end ties if possible, use a triangulated approach from ea side of the bumper [frame tabs or whatever is used] so that end movement is minimized [and thereby minimal unwanted twist stress to the racks].
. . . I never could see the point of those roof top carriers when we’ve got a much more voluminous and especially doubly useful method – and they look meaningful and cut the wind so much better. Or if a seakayak is too big, just pick up one of the many short 2nd hand WW boats that appear on craigslist once in awhile.
[And joking must be inserted: because of the yak’s hydrodynamic shape, at high rates of speed it will actually fly a little bit thereby reducing much of that rack loading, heh heh.]