First of all, genuine failure to understand metaphor is a symptom of ASD (or mere stupidity) and not an indicator of type.
Second, I'll take this opportunity to talk about what I'll pretentiously call the "Ti aesthetic" which creates massive misunderstandings about INTPs.
(Disclaimer: I speak metaphorically here, in fact all talk of cognitive functions is metaphorical, however many fail to grasp that).
INTPs are known for their precision, to the point of being "nit-pickers" or "hair-splitters". This isn't a result of a desire for "correctness", (a superficial Fe-flavoured consensus-based judgement). It's because incorrect usage (unless it's subversive) offends our *personal* aesthetic, in the same way that sloppy attire or tacky home decor or the misappropriation of tools might offend the aesthetics of a Se-user.
Both are subjective judgements about impersonal/objective standards.
In the case of the latter, the (genuine) discomfort might be produced by the clashing of incompatible colours and styles. In sensitive people this can induce feelings of nausea or disgust. INTPs have an analogous aesthetic which operates in the realm of ideas. When you hear an NTP wax lyrical about the beauty or elegance of a formula, model or solution to a problem, you get a glimpse of what I'm talking about. The standard rhetoric about INTPs being obsessed by Truth, is not the whole story. What we call Truth, is anything which resonates with this inner aesthetic (the essence of what Keats wrote on his Grecian Urn). Everything concrete merely reflects the perfection of the Ideal Form (in a Platonic sense). "Beauty" is a measure of the extent to which it approximates this ideal.
Fi-users are similar (which is why they often understand us) but the domain of interest (personal + subjective) is different.
This kind of beauty overwhelms us and seeking out such beautiful experiences, drives us. This is what characterises most mathematicians and physicists: a childlike sense of wonder and awe at the hidden beauty of implicate order. It isn't a world everyone can appreciate so they write such individuals off as weirdos, especially when they frequently fail to pay attention to things in what most consider to be the "real" world.
Conversely, when Ti-users get irritated by the abuse of logic (as some of us have recently with greenfairy) or the abuse of language (e.g. sloppy or cliched metaphors), it is because it can produce an analog of the nausea and disgust of the regular aesthete (sometimes literally!).
INTPs delight in metaphor. Any Ne user must, since Ne plays in the world of metaphor; in the space which connects and synthesises one realm of thought with another. In fact, metaphor/analog is the main way we reach new insights (e.g. Einstein's sub-c train; the way House uses metaphor both to reach diagnoses and to explain what's going on to the "idiots" around him: classic Ne + Ti).
Critical application of Ne + Ti is the way many over-literal abuses of metaphor to model real phenomena (aka false analogies) are undone. "Turtles all the way down" can be seen as either taking a metaphor too literally, or using one to expose the absurdity of unfounded beliefs. In fact, it's doing one to accomplish the other. Ti excels at following premises through to their logical conclusions. Reductio ad absurdum. In INTPs, this often isn't even a conscious or deliberate process - the absurd conclusion reveals itself immediately, given the premise. We can't help but notice, and frequently can't help but comment (though we don't always "show our working", since we sometimes erroneously assume that what is obvious to us is obvious, per se. Also, showing our working involves writing fuck-awful long, dull posts like this one which are boring to read and even more boring to write). This is what is happening in the first example you give. Your friend is using humour to comment on the absurdity of the metaphor (invoking the image of a zombie in a romantic? song corrupts the aesthetic, it jars, and is therefore mock-worthy).
The second example is deliberately using humour to mock the clumsiness of the image (again, an aesthetic judgement). It is also the way we sometimes deal with the discomfort that any appeal to emotion evokes in us.
The third example is just a comment on the absurdity of the musical, which requires one to "context shift" constantly between a relatively realistic portrayal and a highly stylised, surreal one. This context shift, and the accompanying incongruity, creates an unpleasant sensation in those who are sensitive to inconsistency. Personally, I find it hard to switch Ti off in an effort to suspend disbelief for more than brief periods.
(Curiously, this is not incompatible with the INTP love of sci-fi - if the internal consistency of the created world is maintained.)
I am sure you know all this already.
Far from being flummoxed by it, it is usually the INTP who understands that what is merely metaphor is being applied too literally. As an 8 y/o I can remember having a debate with my ESFJ mother about the use of "the heart" in Christian doctrine (as "the seat of motivation", etc). I was irritated (not confused) that an organ which served no function other than that of a pump, should be imbued with so much significance. I understood that the Bible writer was talking figuratively, yet the adults around me believed in a literal interpretation. (You probably know what I'm talking about better than most, Qlip). I couldn't reason with the ESFJ, but a matter of weeks later, the "official" interpretation was changed, at which point she had no problem adopting it. (Of course, we now know that the heart is considerably more complicated than being just a pump, but didn't at the time).
I won't get into fundamental Creationists other than to say that INTPs are not well-represented amongst such hard-headed literalists.
INTPs are the most scrupulous of the Ne users, because Ti demands precision. This is what makes us critical (in a good way and a not-so good way). However, we are not oblivious to the absurdity of this position ( the meta-absurdity, if you will), which is why we mask much of our criticism / disgust with humour (even from ourselves). The expression "if you didn't laugh, you'd cry" comes to mind. The response to incongruity, to a violation of the Ti aesthetic, is a visceral one, an emotional one. Laughing is more acceptable (both socially, and to ourselves) than alternative ways of dissipating that emotion.
Misunderstandings arise when other types fail to grasp that what might appear to be personal criticism, attack, oneupmanship or just inane nit-picking on the part of the INTP (rarely interested in such essentially [anti]social behaviours) is simply our way of expressing the fact that our personal aesthetic has been violated. It is an impersonal assessment resulting from a highly subjective aesthetic judgment. Of course, expressing this discomfort may, in turn, violate the "social aesthetic" of the Fe-user or the "feeling aesthetic" of Fi-users. Hence the not infrequently ensuing carnage.