It is true that there are other metabolic pathways that the plant uses to measure nightlenght. The phytochrome changes it state when no more excitated by certain wavelenghts of light. It is only so that the moonlight plays a strong role in the deactivation of the phytochrome. I am not known with the structure of this certain compound so I do not know how it changes on a molecular scale. It is certain though that the plant measures the night and not the day. On cloudy days the phytochrome is still activated but in a slower rate. It has to be really dark though if you want to upset the plant good eg. no full conversion of the phytochrome.
It is all about deactivation and reactivation and there are many debates on how the plant exactly does that. It is proven though that the moonlight does play a role in the proces but is not a must for the plant to operate properly.
Hope this helps
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