It's done. I've reworked my Agfa Synchro Box to allow both 6x9 and 6x4.5 with a removable metal mask and an additional film counter window for 6x4.5. Materials that I used: 0.5mm thick steel sheet, another Agfa Synchro Box for spare parts, a 12mm diameter o-ring (for covering up the film counter window transplant), super glue, and dull black paint. Main tool was a multi purpose tool for cutting and filing the metal, some aluminium pieces for bending the edges of the mask, and various other standard tools.
What I did is this: made a mockup of the mask from cardboard, transferred it to the steel sheet, cut the mask with my tool, bent it, filed the edges, made it fit snuggly, and painted it. Then I used the paper of a used film to figure out where to put the new 6x4.5 exposure counter window. Then I removed the spring loaded inlay that keeps the film flat in the film plain, drilled a new hole in the back of the box (thanks for the advice with the widening drill, O2Pilot), put the window from the spare box into the new hole, halved an o-ring to get a (more or less) nice frame around the new window, drilled a hole in the film flattener, transferred the light seal from the old box to the back of the film flattener around the new hole, and re-attached the flattener to the box. I call this new box the Agfa Synchro Frankenbox.
Work left: make a pinhole filmholder from the spare box.
Unfortunately it took me so long to work on the box that I haven't tested it with film yet. Stay tuned.