The following is my line-by-line analysis of the covert rhetorical techniques used in the entire paragraph.
The author's entire bias is buried in rhetoric throughout the paragraph. The paragraph includes complications and introduces ambiguities. One might consider this poor style if they did not recognize it as advanced rhetoric. First consider:
Friendship is not a subject we give a lot of thought to.
Note the presumptuous and indirect use of "we give" rather than a more direct "you do not give". Also note the use of "not" being placed further away from the the verb. Compare with the following:
Friendship is a subject you do not give a lot of thought to.
Clearly, the original sentence is more easily acceptable to a reader. The next sentence is rhetorical:
As the saying goes, we know who our friends are.
Is there really such "a saying"? One could just as easily say, "As the saying goes, we only know who our friends are when the going gets tough." The next sentence introduces a false "we've probably never considered" along with an arbitrary statement:
But we've probably never considered the difference between, say, "convenience friends" and "crossroads friends."
The "but" is an empty segue that only seems to make sense. This is a false "we've probably never" because the referenced author is the one who is defining the difference. It would be like someone introducing Einstein's seminal paper with "we've probably never considered the theory of relativity...but Einstein has...". The word "say" hides a carefully crafted and deliberately persuasive point within an informal, impromptu voice. And the final statement is the target statement:
Judith Viorst has, and the classification of friends she outlines here will probably ring true to you.
The sentence is understood as follows:
"Judith Viorst has [considered the difference], and the classification of friends she outlines here will probably ring true to you.
Grammatically, it's similar to the following:
"Did you eat the pie?"
"I did, and it was delicious."
This statement "sneaks in" the "fact" that Judith has considered such a "marvelous thought" that "the rest of us dummies never thought about". All of that within a single word: "has". That "fact" is quickly buried in complexity and ambiguity, so by the time you figure out what it means, you can forget that the author said something questionable. In other words, the author's writing is highly rhetorical, and she is hiding the rhetoric with complexity and ambiguity.
This is not necessarily "bad". In fact, it's quite an impressive study in the use of effective, covert rhetoric. This construction is idiomatic of positive book reviews as well as book-selling copy on both the back cover and front jacket flap.
sometimes choices make you
It means that sometimes the choices you make influence who you become as a person.
As noted by @Sam I Am, this is not a normal phrase. It is designed to be the reverse of the first half of the sentence (you make choices), and seems to be ironically implying that while you expect to have control of your decisions, sometimes those decisions can effect (control) you.
In this case, it is also implied that these choices are especially important, hard, or have dramatic (possibly unexpected) results. Less obviously, it is likely implied that some portions of these choices are negative in some way (though this may not always be the case).
Example
During your childhood, you become a delinquent, and end up committing a crime that lands you in prison for 10 years. This choice may "make you" into a fundamentally different person than if you had not gone to prison. Perhaps you now feel compelled to work helping criminals give up their lifestyles (because prison had such a negative effect on your life) rather than if you had not gone to prison and become, say, a wealthy banker.
Alternate Phrasing
Is there any other examples or metaphors that could be meant by that phrase?
The closest I would say would be:
"You (We) are the sum (total) of (all) our experiences"
Meaning what you experience in life shapes your personality, outlook on life and general approach to living.
Best Answer
From original question
If you saw something confusing on a street sign, you might point and say "what does it mean by that".
Here, "it" would refer to the sign. You are treating the sign as if it were a person who had said something. So it's very similar to sentences like "What did he mean when he said that?"
This isn't particularly common. If you are reading and trying to understand a book that has a lot of confusing sentences and it's like the book itself starts to take on an evil identity...it might be more common. :-)
As for "What does it mean that (...)", there are rare cases you might hear it as a kind of question to provoke thought, where you're not expecting an answer (e.g. a "rhetorical question".)
But if you're really asking about what something means, "What does (...) mean?" or "What's the meaning of (...)?" would be what you'd want to use.
From updated question
If you ask "what do you mean by ____" then you are suggesting the person has said something you want them to explain. But "what does ____ mean" could be asked of someone whether they've said anything or not. You're just asking a question about the general meaning of something.
In usage, "What do you mean by that?!!?" can be a strong negative reaction...usually when someone has said something that the person feels was meant to be insulting even if it wasn't "obviously" so. So it's not really asking for clarification, because the speaker has already assumed it was meant in a bad way.
But it can also just be a polite phrase asking what someone meant.