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.
Can you explain to me how you would do that outside of a laboratory setting? The real answer is that it's an amorphous fluid. It is a single object rather than discrete quanta.
What's happening is that you're trying to identify the exception and make it the rule. Yes, you can figure out how many moles of water are in a volume at a certain temperature and pressure. That's not really the point, is it? When people pour glasses of water, they aren't thinking in terms of moles. The word is noncountable because it was invented by humans far before any sort of chemistry was discovered. That usage can change, sure, but do you really think that the average person will ever see it that way?
Alternatively, are you thinking in terms of measuring volume? That's definable, but it's also not what is meant here.