Hi Simon. Have the same boat. And the same problem. But I have sailed fine with this transom rot, and do not consider it to be a big issue.
There is epoxy foam that can be used to fill in the gap after making holes to remove the wood. Or a supporting structure could be made on the inside of the hull/boat out of wood. To prevent compression(maybe only a consideration when on the hard)
Even if you or the next guy decide to use a vibrating saw to cut 15 to 25 cm from the edge all the way around the inside of the transom and then get the wood out, then fill in with new wood/epoxy or epoxy foam, I would consider it doable and not too bad.
The prosess as I see it(experienced with epoxy work, but no expert):
1. Get the transom through-holes out
2. Cut the inner laminat. But not too much around the edges, so you are able to interlock new layers fiberglass and epoxy later. Get the rotten wood out.
4. Sanding around the edge of the cuts, to make a bevel, both at inside the boat and on the cut out. (Renting/having a good sander for this, or an angle grinder with flap disc. And a shop vacuum cleaner and a strong fan ventilating to the outside can help greatly with the comfort)
5. Let id dry out for some weeks, or speed up the process with dehumidifier.
6. See if the surface where the core was is oily, try to clean with spirits or aceton. Clean everything else as well.
7. Get new core material in, either foam boards or wood with a good amount of epoxy. or epoxy foam. Or a combination. Make holes where needed to fill in more thickened epoxy/foam.
8. Make temporary wood planks to support while the epoxy is curing. Glue in the cut out transom inner laminat back(maybe with core material glued onto this piece). Press it in place with the wood planks screwed across the inside transom.
9. Laminate over the the inside transom cutout bevel.
10. Sand the inside transom again and laminate over the whole inside transom.
11. Paint.
12. Happy sailing :)
Could also do it on the outside, but think that fiberglass layer is thicker.
PS. Paid for a membership, just to reply to you. :)