It doesn't work that way - there are no "layers".
if there is no underlying data it can not retrieve CF settings and it clearly does.
if there is no influence from CF, how do you explain scenario 2?
in my experience there have always been conflicts between CF and CHDK.
if i encounter those for a specific setup I usually try to avoid setting that value in CHDK and see if it can be solved by setting it in CF.
the trick of forcing values by setting similar values in CF and CHDK is something that I don't use a lot, but for reboots in combination with zoom it seems it's needed again.
i also used it the other way round on my m10 (setting iso differently in CF and CHDK) to reduce max exposure.
i actually want to adapt the UI script so it does not use percentages anymore, but rather the fixed values CF uses on my S95 to prevent even small differences during a reboot/zoom/rezoom/focus cycle.
although i'm not certain that would change anything i think it would at least make chances smaller that there is a difference in some or other calculation.
since my goal is to work with the reboot function @ 24 days i wouldn't want to discover that is was for naught due to small zoom differences that I haven't spotted on my previous tests.