Depends on if you're using water to include types of water (if, like a maniacal madman, you have mixed Evian, Buxton and Harrogate mineral water into one jug). Then 'i mixed fewer waters' or 'there are fewer waters in that glass' would be valid.
To be clear: I'm not the person you replied to, just someone who finds it quite interesting (in the same way that the plural fishes is valid if you're talking about different species of fish).
And yes, I know prescriptivism is bad, but also it is quite fun.
Eh, you wouldn't use the noun water to refer to atoms of water. 'How many waters are there?' to refer to atoms of water is the statement of someone deranged
I think you're too rigid with your definitions. I just showed you an example of where water, usually not countable, is used in a plural form in real world usage.
Regardless of whether the noun is countable, the thing itself (water, air) absolutely is countable, i.e., comes in discrete measurable amounts, which is the more important issue here.
you used a HOMONYM because words can have different uses. "water" meaning an amorphous fluid of dihydrogen monoxide vs "water" meaning discrete bodies of water. You can count bodies of water but you cannot count how much water is in your glass. If you want to use water as a countable, that's fine, but you would be using it in a way that most people don't intend.