The international standard 40 foot ISO container width is 2352mm (92.5 inches) and sometimes the door is somewhat smaller at 2340mm (92.1 inches). With your packaging or trailer and a vertical yacht this is going to be cutting it very close indeed.
If 2 boats are placed on a 40 foot trailer it cannot be on or in a container that can be transported by vessel. The extra tall high cube containers still do not give enough volume for 2 yachts of that beam and height.
One thing that is very important is your insurance. Cargo insurance is a really sticky subject and the first time I read the fine print I my blood pressure shot through the roof because I thought I was being ripped off. Even with an expensive policy ($2K or so) it turned out that almost nothing was covered. In the end I opted not to pay insurance and was quite lucky when nothing happened. But I subsequently got to know the cargo manager for a major Taiwanese cargo company in LA (one of the biggest containerports in the world) and he regaled me for hours with stories of lost and damaged containers and other related stories.
It pays to get a good agent involved to get both insurance and cargo location sorted out. An optimal position in the stacks is tough to ensure otherwise. Outside top containers occasionally go overboard, bottom-of-the-stack or outside containers sometimes get shrunk or suffer waterdamage.... the list of possible problems is pretty long. The ones that worried me most were having your container absorb some wonderful (and permanent) odors during transport particularly when crossing the equator or sailing in the tropics. Getting a "Linie Aquavit" is good for alcohol but crossing the equator next to a container full of decomposing natural products will leave your upholstery retaining the smell for a long time after trip