This looks like a good opportunity for a DIY solution.
Also, a while back there was a company making custom "matched" luggage for the Mazda Miata (to maximize the limited trunk space), and one of the included items was a round storage bag with a hard bottom that fit the spare tire. Seems like a dry-sack with a plywood insert would serve a similar function.
You could use some thin plastic rounds (HDPE, PTFE, cutting board?) and make a "tool board" like that shown above (or even more than one) and mount it in a cheap dry-bag of the appropriate dimensions and build your own little tool kit, fitted out just the way you need.