A boat supported between two crests is not in freefall, otherwise it would not be "supported". While it is true that such a condition essentially impossible it is a reasonable assumption that factors in reasonable safety margin. Few people would want a kayak built exactly "strong enough" to handle the expected conditions because chances are it would not last very long.

Bicycle racers like bikes that are just "strong enough", because it is not a big deal if they have to retune or replace their bike after every race. By the end of a race fatigue has pretty much made the bike unusable for the next race without major work.

While I have never paddled in a condition where my kayak was bridging between two waves, I have often been in conditions that would cycle my boat through a lot of forces. Spending a day playing in breaking surf or paddling for hours into a head wind will produces a lot of forces trying to bend my boat one way then the other. This cycling of forces creates the perfect conditions for material fatigue. While a given boat may be strong enough to handle those forces 100 or 1,000 times, fatigue may break it after 1,001 cycles.

This is one reason to "over engineer" a design. By making a design much stronger than it needs to be the forces are less likely to stress the boat in a manner that will cause fatique, and if it is stressed to that point it may be able to handle more cycles.

One of the biggest advantages of wood over other materials is that it is highly resistant to fatigue. Making the wood carry the majority of the stress will make a longer lived boat than one where the fiberglass and epoxy carries those loads.