Kyle, Yes where the keel cutaway foot angles upward. (This where the bulk of the ballast is located) If you look at both trailer pictures that you posted earlier you can see each sets a little different, one is slightly forward of the front axle and the other boat much less so. The length of the tongue on the trailer will effect the weight on the hitch. This could very well be the reason different trailers have the boat placed differently. The position of the beams won't effect the C/G, the position of the load (boat) will. I would try to space the crossmembers evenly with relation to the upright positioning
The one trailer that I built I took measurements of the bulkheads on the hull and made the uprights set on or very close to these. I thought that was important at the time, in retrospect the weight of the boat is on the keel and the uprights are for balance parked and lateral support running down the road. The bow support I think is most critical, I would make this adjustable or temporary until you know the exact placement of the boat on your trailer. This support, properly set adds support to the tongue of the trailer. If you add a attached ladder to this you won't regret it, I had the forward hatch fly open towing home and no safe way to get on deck. In the pictures of Schnell the blue boat, it appears to not even contact the bow, but then Mike was using this as a cradle preparing to launch. The yellow hull boat doesn't appear to have a bow stop or support, that makes me nervous!
Kyle, On two of my trailers the rear most crossmember is behind the rudder shoe, the shoe doesn't contact the support on either of them. The third trailer is cut short because it was designed as a float on. Something to keep mindful of is you are going to scrape and paint the hull set the keel on a couple 2x4s placed cross ways on the keel support beam so you can paint the keel bottom, then crank up on the support pads and relocate the 2x4s. .
If your trailer has spring suspension, the rocker or equalizer between the two springs actually equalize the weight between both axles. this will make an exact measurement not so critical. Think of the advantage of moving rearward on a see saw as a child and the advantage gained so that you could hang your partner in the air!!! Moving 5500lbs 2 or 3 inches is a lot of weight adjustment.