In answer to your questions:
1- The new TI support cradle should prevent any possible scupper damage of the type where the top deck of the hull is pushed up. Essentially the weight of the TI and accessories was pushing the scupper tube through the deck. The cradle spreads the load more evenly. It will not prevent operator error where the scupper cart uprights damage the internals of the scupper tubes. Hobie have added a reinforcing pipe to prevent this in the forward scuppers.
2- I have often taken my scupper cart (Trax2) on the TI without problem
4- My TI has been stored on the trailer cradles, right side up, for the last 3 years with no damage. I do have bow and stern supports though.
5 -iComfort seat pads
I have used scupper carts with all my Hobie's and have had zero issues. The advantage of a dolly cart is when retrieving as it is difficult to get a scupper cart back in when on the water. A dolly cart just slides under and makes retrieving, especially in Winter, much easier and drier!
If I was buying a cart today I would be opting for the new Trax cart with the 30cm balloon wheels and getting the support cradle plus a set of the HD Wheeleze foam wheels. That way you have all terrains covered.