I do not have any experience with Boat lifts, however I have spent hundreds of hours configuring and reconfiguring my trailer for two AIs. Boat bunks, cradles, & finally PVC.
What I found with having two AIs is that the bottom hull contours are different on each boat (different on my two). The boat bunks worked ok, but do not conform to the hull shape. One of my AIs sat fairly well on the bunks (7ft bunks in the back, 3ft toward the front), but the other one did not. I would think that leaving the AI out on a lift in the heat with wooden bunks may cause warping. Add a tarp over the boat & the heat probably gets even hotter inside...
I recently switched to the PVC method using 2.5" 10ft and couldn't be happier. I wonder if you could build a rectangle frame that would go on your current set up that would hold the PVC tubes.
Just my two cents, good luck!