I'd like to briefly address three of your points.
1. "A result of insufficient up-front design"
Common sense (and several books and bloggers) tell us we should strive for the simplest, cleanest design possible to address a given problem. While it's quite possible that some code is written without sufficient work on developing an understanding of the requirements and the problem domain, it's probably more common that "poor code" wasn't "poor" when it was written; rather, it is no longer sufficient.
Requirements change, and designs have to support additional features and capabilities. It's not unreasonable to anticipate some future changes up-front, but McConnell et al. rightly caution against high-level, overly-flexible designs when there's no clear and present need for such an approach.
3. "A dangerous activity that needlessly risks destabilising working code"
Well, yes, if done improperly. Before you seek to make any significant modification to a working system, you should put in place proper measures to ensure that you're not causing any harm - a sort of "developmental Hippocratic oath", almost.
Typically, this will be done by a mixture of documentation and testing, and more often than not, the code wins out, because it's the most up-to-date description of the actual behaviour. In practical terms, this translates into having decent coverage with a unit test suite, so that if refactoring does introduce unexpected problems, these are identified and resolved.
Obviously, when you seek to refactor, you're going to break a certain number of tests, not least because you're trying to fix some broken code contracts. It is, however, perfectly possible to refactor with impunity, provided you have that mechanism in place to spot the accidental mistakes.
4. "A waste of resources"
Others have mentioned the concept of technical debt, which is, briefly, the idea that over time, the complexity of such systems builds up, and that some of that build-up has to be reduced, by refactoring and other techniques, in order to reasonably facilitate future development. In other words, sometimes you have to bite the bullet and go ahead with that change you've been putting off, because otherwise you'll be making a bad situation appallingly worse when you come to add something new in that area.
Obviously, there's a time and a place to pay off such things; you wouldn't try and repay a loan until you had the cash to do it, and you can't afford to go around refactoring willy nilly during a critical stage in development. Nevertheless, by making the decision to address some of the problems in your code base, you save future development time, and thus money, and maybe even further into the future, avoid the cost of having to abandon or completely rewrite some component that is beyond your understanding.