I pondered the same thing.  I ended up glassing the transom prior to the hull, overlapping onto the sides only.  Then, when I glassed the hull, I overlapped a bit onto the transom.  Last, when I did the deck I overlapped down onto the transom per the picture.  With the multiple layers on the transom, it took a number of fill coats back there.

If I were in your position, I'd glass the transom first, overlapping sides and bottom, then glass deck overlapping the transom.  

   Great advice - thank you Mark.  Looks like you left some glass to trim with your overlap on the side.  Did you trim that with a razor knife and then sand the edge and recoat?  And was the fill coat on the transom the same idea?  Try to feather out the edges of the glass with a sander and keep recoating with clear epoxy to get an even surface?  I did a terrible job with this sort of the thing on my Skerry with the glass tape in the stems.  I didn't realize what I was supposed to be doing with feathering and filling.

Today I glassed the deck of my current build.  This is the same process that I used on the Kaholo. 

Mask the boat along the line where you want to overlap to end, then drap the glass.

Next, wet the glass out down past the edge and partially onto the masking take.

Next, while the epoxy is still green (not tacky but still soft enough that you can dent with a thumb nail), take a sharp razor and cut the glass along the edge of the masking tape, and pull the tape off.  The resulting edge with be straight and pertty clean. 

Tomorrow morning, I will hit the edge with a light hand sanding to knock it down and eliminate any roughness.  Then, I will put two fill coats on the deck making sure that I cover the edge.  After that, the edge will disappear with just a bit of sanding. 

   This is excellent instruction and clear photos - thank you Mark!

Michael