Keep it simple I recon. With a third and possibly a fourth yak to be added to the fleet shortly I’ve been thinking about doing something like this also. I cant see why you cant just have a box trailer with some gal pipe on either corner to stop the yak moving side to side. I don’t really see why you have to have a divider between each of them.
If they are all plastic yaks they will hold each other in place ok if they are tied down securely, well mine do on the roof of the car anyway. Or at most you could add a cross beam to the pipes so you could have two and two down laying flat.
At least this way you can still use the trailer for trips to the tip etc without having to remove bits and peaces.