I did a better job of fixing the pattern maker's dowels with the next baseboard connection. Practice makes perfect.
This time, I drilled a small pilot hole through both baseboard frames while they were clamped together. (There was only just room to get my small Makita drill in to do this - something to maybe plan better in future!)
Thus, when the frames were unclamped the pilot holes were exactly aligned where the faces meet. Then, using these pilot holes, I was careful to hold the drill perpendicular to the face while I used the forstner bit to drill out the pockets for the dowels.

Much neater!

Since the pockets were more accurate I went ahead and screwed the pattern maker's dowels tightly into the pockets and offered the boards up to each other. Clunk! Perfect fit and alignment is acceptable.

So I now have the three main frames joined and bolted together on the trestles.

Next job: Construct the twin track bridging section to span between the horns of the "U". It will be an H cross-section of 9mm ply with 78mm deep cross-bracing below the track bed. The taller sides provided by the H should prevent the 1440mm long bridge from sagging in the middle.