Thank you, and Congratulations on the purchase of your new TI, you're going to really enjoy it I'm sure. If you could post some pictures of your trailer, I might be better able to understand your questions but I'll try to answer to your immediate concerns for now.
difference between a TI and AI are significant factors as to how we transport these boats, as is the types of trailers we have available to us. The height of which your boat sits on your trailer also plays a big part in what angle it travels when sliding on and off.
That being said, I've found that on my SUT-350-S Trailex Trailer, I must have the rear saddle fixed to the trailer to have support back there for the entire boat when launching and retrieving from either a boat ramp, or on and off the Appel Cart.
Sounds like with your "flatbed trailer" you may already have that rear support covered and could possibly make a detachable cart for the back end. I'm sure there's a way you can work this out.
The aluminium support tubes covered with the pool noodles on the Appel Cart cart are in line with the scupper holes, but not for that reason. There are two parallel channels running down the underside length of a TI. They were molded into the hull to help the boat track in the water and to give it more strength underneath. The spacing on my support tubes conforms to these "tracking channels" because it's a strong area to support the boat.
The balance point for the TI is forward of the scupper tubes. There's no advantage having a locking down tube holding the cart in this area because you must place the cart directly under the balance point to move it around comfortably - similar principal to the fulcrum on a see-saw.
Hope this helps to answer your questions, have fun with your new boat, post some pictures when you've got your trailer worked out