The slickest wheel clamping arrangement (from my uniquely warped perspective) locks the wheels but leaves the bike's suspension completely free. The clamping force should be applied to the tires to avoid damage. I can understand the appeal of a rigid bracing point under the engine, but you really should think of a CT70 in terms of unibody construction. That means that the design, while very strong & light, has weak points. You wouldn't flatbed a car with a jackstand placed tightly beneath the engine and the suspension at the top of its travel, for obvious reasons. Nor would you attempt to lift a car using the floorpan, or transmission, as a lifting point. Likewise, these bikes are designed to take all loading through the wheels only. Yes, I agree with Dan that the rigid support point beneath the engine will be rough on the engine guard & engine cases. Will it fatally damage the bike? probably not. However, consider that the engine & frame take will the full hit of any vertical motion with the suspension removed from the system. Also, the frame is not designed to asbsorb shock loading from below.
When clamping the tires in place, working room becomes the deciding factor. That's why I recommend using the front wheel as the main clamping point; you can cradle the tire above and well below the centerline, preventing any wheel rotation and vertical movement. Configure the crude "vise jaws" to roughly resemble the letter "K", with the upper left section missing. Long carriage bolts go in the upper right and two lower points. With the lower front bolt firmly against the tire tread, the wheel is positively located fore & aft. Locate the upper RH bolt above the wheel centerline, such that it takes a bit of force to pivot the vise jaw into place to insert the bottom LH bolt and the wheel is locked into place vertically & horizontally. (This is described from the RH side of the bike. Obviously, the LH side would be a mirror image).
Clamping the rear wheel is more difficult, there's little working room. Your redlined concept should be very workable, though you may have to do some complicated trimming to clear the sprocket, chain & rear brake setup. That doesn't address vertical wheel retention and there's no easy way to locate a long bolt above the centerline of the rear wheel. For that, I'd use a ratchet strap over the tire tread. The tires are a nice failsafe in that the bike will be securely retained long before too much force is applied and the suspension takes all of the shock loading as you go down the road. This setup borders on overkill, you might be surprised at just how stable the bike is with the front wheel locked in place alone, but you still have to consider the black & white tax collectors. For that, I'd retain the ratchet strap you have over the frame but relocate it over the seat with extra some padding, and loosely (just tight enough to keep it from flailing around at speed), much like a trailer safety chain. An expansion spring, located on the leading edge of your carrier (where it can't be seen while driving), would allow your ratchet strap to have some "give", without compromising safety or legalities.
I hope this doesn't come across as suggesting that you reinvent the wheel. Your basic design is 85% of the way there, as-is. Adding four movable steel plates, five carriage bolts and eliminating the under-engine platform is what's involved. Best, I think, to do the work at the beginning and enjoy the fruits of the effort for years to come. Survivor bikes in that condition aren't easy to find.
attention to a very sweet Topaz Orange Minitrail and kissing it with their frontend of there vehicle!!!! OUCH 
