Yes I believe I'm sufficiently convinced now...
1) Hm...did you just prove that (if not in M mode) the camera decides flash power after CHDK has overrided Av and Sv?
2) I guess (because I don't know better) that automatic flash power is very difficult to implement in M mode. A finer manual control of flash power in M mode sounds like the logical next step, and in search for that I'd start by trying to find a propcase that correlates with this finer flash power level. From
http://chdk.wikia.com/wiki/PropertyCase you can see we already know of several propcases that have something to do with flash (121, 122, 127, 133, 141, 143, 208 for the Digic III propset)... this one should be new, and likely must be read during the shooting process.
If propcase control doesn't cut it, I'm afraid firmware disassembly analysis is required for each and every camera model and fw version, potentially a lot of work with no guaranteed result, meaning an eager & skilled developer is required.