Since it’s a very long and complex question, I’ll do my best to begin an answer.

Short answer :
In this context, your previous assumption was correct, and the sentence means "He poured himself little glasses."

EDIT: After reading Catomic comment and checking the novel, it was indeed "Small glasses were served." that was meant by Flaubert.

Déjà les farceurs commençaient leurs plaisanteries. Beaucoup chantaient. On était gai. Il se versait des petits verres.

Long answer :

Question 1 : Am I OK to understand the basic form of verser this way?

It is in fact a bit more complex. In your example you are right, but the fact that R2 though gramatically correct is absurd, will lead anybody to look for an other meaning.

Question 2 :

2.1 : Do we say, for example, that the place of subject for courir is filled by une rumeur in the first sentence and filled by Il in the second but "held for" une rumeur?

Une rumeur court.

Il court une rumeur.

In the first, the subject is "Une rumeur" and in the second it’s "Il", regardless of what it stands for.

2.2 : Do we say that Il "refers to" une remeur? Or does an impersonal pronoun never "refer" but only "hold the place for" some thing or other?

Here "il" has the same value as in :

S1 Il est tard. -> It is late.

The impersonal pronoun holds the place for "The current situation is that…".

2.3 : In the second sentence, do we say that the subject is Il, or une rumeur, or both Il and une remeur?

In the second sentence, the subject is indeed il.

Question 3 :

S2 Il se prépare. -> He gets himself ready.

S3 Il se prépare une omelette. -> He cooks himself an omelette.

S4 Il se prépare quelque chose de grave. -> Something serious is about to happen.

You get that what comes after the verb can totally modify the meaning of a sentence. I do not have an comprehensive answer on why it is so yet, but it’s worth trying to analyse this.

Question 4 :

Given 2.2, answering this becomes irrelevant.