I think you’re referring to ENR 1.1-4.2. I see a distinction between the requirement to ‘operate’ in sight of the ‘generic’ ground or water whenever VFR at or below the higher of 3,000’ AMSL and 1,000’ AGL, which I think is a requirement mainly aimed at reducing the general risk of colliding with the ground or water, and navigation and position fixing requirements, which I think are mainly about not getting lost (but will help you to know whether you’re above or below that line in the sky).
I’ll try to overthink this in a different way: If the operational requirement to operate in sight of the ground or water when operating VFR below that line in the sky has an exception - “unless the pilot can’t see any ground or water” - it’s a meaningless requirement, is it not?