There are homeomorphisms that cannot be considered as stretching and bending (don't know what the proof of this should look like, as we haven't defined stretching and bending formally, this is my major concern here) - see the bottom of page 22 in A guide of topology by Krantz.
Even if we accept that some homeomorphisms cannot be understood as stretching and bending (whatever stretching and bending means), we assume that all stretching and bending that can be represented by homeomorphism - why is that? Has anyone proved it?

I’d say just leave it as an informal, but powerful way to intuitively reason about topology.
In an analogous situation, computability and decidability of problems can be defined mathematically, but we never can prove mathematically that these definitions really grasp our intuitive notion of what can be computed. The Church–Turing thesis is a meta-mathematical thesis which says that those definitions really do grasp our intuitive notion of computability.
If viewed as a philosophical statement about the nature of our universe, there really is strong evidence in favor of the Church–Turing thesis: For one, all attempts are formalizing computability have been shown to be equivalent. And on the other hand, as one develops a sense for what is Turing–computable, one finds that anything that looks intuitively computable also looks Turing-computable and vice versa: The intuition for the mathematical concept of computability starts to overlap with the pre-mathematical intuition of computability.
And this is the point of my answer: I think with topology, it’s much the same – only that the thesis in question doesn’t have a name (and is known to be slightly false). If you just start doing topology, you will most probably find that your intuition for bending and stretching and your intuitions for homeomorphisms start to overlap a lot. I think this is the best justification for the cited non-mathematical description of topology as a field.
And now, to address your concerns regarding this:
And as you said, the thesis doesn’t work out completely and I share your concerns about using it to prove stuff. Luckily, I found that most of the stuff I have seen proved using visual bending–stretching arguments can really be proven rigorously using real mathematics. This really helped me a lot to accept the attitude. Maybe this will help you as well.
So my advice to you is to not lose to much sleep over it: Don’t think of it as a definition of the field, but rather as a description and don’t expect stretching and bending to be defined formally.
You may either regard topology as mathematics which formalizes reasoning about things like bending and stretching, or you may regard things like bending and stretching as intuitive notions which help you reason about topology.