"Spring Clamps" ??? Did you mean sheer clamps, as in the thin strips of wood glued to the inside top of the side panels? If so, yes, the transom (stern panel) is glued to the butt end of the sheer clamps and inside of the sides. The bottom and sides shall overlap the transom (stern) edges.

Sorry yes, sheer clamps. fitting the transom to the sheer seems odd in that my sheer clamp is 1/4 inch shy of the end of the side plywood. (per directions)   The pre-drilled holes in the sides of the plywood wood indicate that the transom should meet up with the sides and not be push into/onto the sheer clamp.

Ah, I used 1/4" Western red cedar strips for my transom, so it fit. If you're using 3mm or 4mm it will sink in a tad at the top of the sides when properly glued to the sheer clamps. Do not sweat it. Trim off the overhang with a sharp low angle plane, or a sharp utility knife. Course I would just reach for my go-to tool for making minor :"adjustments" - a nice piece of 1 x 2 with a strip of #40 grit air file paper attached with 3M 77 spray glue. It is a wood grinding beast . . .

If you do not use the 1/4" strips and only use the plywood transom, you should consider adding a "shear" clamp across the top of the transom so the deck can be glued down and sealed.