Well, it´s standard usage to think of the comma as a pause, similar to how our
"e" with a function of "vírgula" (it happens sometimes).
It seems like my very last example with "where were" mislead more than it helped, but forget that one and think of the first part of my posting. What I meant is that some kind of collocations come to mind by repetition. We see or hear a construction and we get used to it, we get to know which is which.
Back to the crux:
"I found a narrow room, [whose end] and side windows were closed by falling stones."
Here, we can distinctly see that whose and end are a pair (we could think of whose as an "antecedent"), they work together in the sentence. By pausing at "whose" it would turn it into an isolated piece since the first comma is a pause as well.
"Whose" indeed provides information about "end", the pair lead us to ask,
Whose end is that? The end of the narrow room.
"end and...", In its turn would make the second part ambiguous, which is what we should avoid.
I hope this clarifies things a bit more.