I've never cited a software I didn't write myself, simply saying trust this software, here's the reference. I wouldn't trust a result from Sage any better than one from Mathematica, simply based on which system produced it. I'd trust that x is a solution of an equation if substituting it back verifies it. I'll trust that two graphs are isomorphic if the software gives me a vertex permutation that makes the adjacency matrices identical. It doesn't matter how that isomorphism was computed.

When publishing work, I'll aim to make it verifiable this way.

I believe the vast majority of the use of these systems is not of the type when one needs to blindly trust the software and refer back to it in the paper. At least in my field (physics) it isn't. Yet I use programs like this daily, and I clearly depend on them for my work.

Most of the functionality available in Mathematica (or, I'd argue, most similar systems) are not of the type that one needs to cite. They either use standard and well known algorithms that are available in a multitude of systems (do you cite the methods for matrix multiplication or eigenvalue computation, and would it make a difference?), or the results are much easier to verify than to compute.

In those cases when I need to rely on a published method, like you mention, the method is very unlikely to be a built-in part of any system. So I either need to re-implement it, or use the original code of the authors. If the authors implemented their method in Mathematica instead of Python, does that make their program less reliable? No. It's still a published method, anyone can verify it.

My point is that I hear this argument about Sage very often, and the typical generalization is: "if you used Mathematica for your research, that's wrong, because it's not verifiable". This is a fallacy. It completely ignores how these software are used in practice, and implies that results from open source software are somehow magically reliable (they're not) and don't need verification (they do).

I've yet to come across a situation where the argument does apply at all: point me to a paper which goes truly wrong by citing Mathematica/MATLAB/Maple/etc this way.

I would expect that the difficulty of the port could vary widely between different use cases.