From a logician's point of view, logic is far more than just a tool!! But that's probably a topic for another time...
Certainly, I think people would (or should) agree that logic is at least at very useful tool. The first answer to the question you linked to has a fair point: for most mathematicians, the logical abilities are not as important as creativity. Often times, in constructing proofs on your own, it's not sufficient to just try every possible combination of inference rules that could be used on those axioms. A lot of proofs require you to construct certain mathematical objects with special features, or you need to set up definitions which will be useful later on, and this process is (arguably) a creative process. Once you have the idea behind a proof, constructing the logical argument to follow is more like filing paperwork: it needs to be done, and students need to learn how to do it, but once you know it, there's nothing technically difficult about its implementation.
Furthermore, logic can only take you so far in terms of belief revision (as is well known in theories of belief revision). If you start with axioms which intuitively seem to capture the concepts you're after, and it turns out someone churns out a proof of some highly counter-intuitive result about that concept, logic won't tell you whether you should do a modus ponens or a modus tollens; that is, it won't tell you whether you should trust your axioms and keep the counter-intuitive result, or whether you should reject the counter-intuitive result and revise your axioms (or even your logic! but let's not go there). So when you're doing serious mathematics, you need a kind of intuition regarding whether the results you obtain seem to make sense, given what you're trying to describe.
With that said, there are probably plenty of cases where by now we've dropped the modus tollens option entirely, and just work axiomatically. There might be cases, e.g. set theory or computability theory, where we've changed our intuitions regarding the original concepts to a point where we've simply come to accept or even define our intuitions to be just what the axioms say. Even in these cases, of course, one still needs some kind of intuition about how the axioms work, but the above dilemma occurs less frequently.
To answer 1): in my experience, most math undergrads are required to take a discrete math course where they cover certain basics about logic, number theory, etc. So they learn some, but often times they're only expected to learn just enough.
To answer 2): it's true, I think, that a lot of people have the wrong impression of what mathematics is. Most people I've talked to who haven't studied serious mathematics think we just crunch numbers and do complicated integrals all day (which may be true of some, but certainly not all). Of the people who have taken serious mathematics courses, or who have taken courses which talk about serious mathematics (e.g. philosophy of mathematics courses) tend to get the impression you seem to get. Most mathematicians, I would think, get the intuitive content of the axioms/concepts, and work with those first and foremost; then they translate this intuitive content back down into the level of rigor. But that's not to say that all there is to logic is filing paperwork!