That's why we went through the whole process of figuring out and documenting what worked for each camera :
CHDK MF Testing Xref
And if IIRC, somewhere in this thread we decided not to automatically set AFL or MF in the CHDK SD override menu. Or maybe we decided that in the IRC conversations at the time.
The final compromise was the get_sd_over_modes( ) function, which at the least allowed a script to make a somewhat intellegent choice about handling manual focus.
That is an impressive quantity of work! I am not a developer, but I guess, that there are too many factors regarding the manual focus function, to be able to insert it exactly the same in every camera firmware.
Good luck in the future with the project and hopefully Canon will create cameras that will be easier to tweak.
