The warning regarding the AF led when debugging is not explained.
Do you suspect it is not intended to be continuously on or do you think users may have AF-assist enabled ?
Both, but mostly the second. I'd guess the AF isn't meant to run continuously, but I'd also guess it has a lot of margin. Blinking it for debugging should be fine (many people blinked out their firmware using AF), but not good to do if someone is actually trying to take pictures.
The duration of NOP's depends upon whether caching is enabled.
Presumably we do not have any control over caching ?
We certainly do. Most ports disable the caches in loader/resetcode/main.c copy_and_restart() and re-enabled them in platform/<camera>/<sub>/boot.c boot()
The state when CHDK is booted may depend on exactly how it was booted.