About the specific questions in your query.
The reason that people don't say 'Four glasses of beer' very often is nothing to do with the grammar of the sentence. In fact, with beer, you would normally also specify the type or brand, rather than just 'beer'. But to get back to the question of quantity, the fact that we don't say 'Four glasses of beer' is more to do with the fact that it's not very informative or helpful. You'd say ' A pint of beer/ two pints of beer/ a half-litre of beer/ three halves of beer . On or in other words, you'd say what size of glass you want. The same with 'bottle' - if it's a drink that is usual served in a bottle then you don't need to say it. It's the same with 'coffee'. Coffee is usually served in a cup, so you don't need to say it. You'd say 'two black coffees' 'two large coffees' etc.
Regarding the question of paper, yes, you are right that the 'substance' paper is uncountable, but often we use that word with a slightly different meaning .
'Two papers' doesn't mean 'two sheets/pieces of paper' . As Sandrah suggests, if you hear 'two papers' it's probably in an academic context, and it means something like a thesis or dissertation. It is also used countably for parts of an exam. Some examples.
eg 1. Paper was invented in China thousands of years ago.
2. When you go to the shopping, can you get me some paper?
3. When you go to the shopping, can you get me a paper?
4. Which paper do you prefer - the plain or the patterned one?
5. The exam is divided into three papers - reading, writing and listening.
As you can see in 1 and 2 , 'paper' is uncountable - this refers to the substance. In 3, the listener would understand 'a newspaper' = countable.
In 4, you are talking about 'types of paper' = countable. In 4, the word 'paper' refers to parts of an exam = countable.
I hope all that answers your questions!