Yes, yes they are.
Lots of engineering effort goes into making this be true.
TFA argues that you can't control the inputs perfectly, and so the behavior may differ if you fail to control the inputs. Yeah sure.
But the answer to the clickbaity question in the title is simply "Yes".
Even the specific example in the article, the non-determinism was treated as a bug and was fixed (since by 2004 that was definitely a regression - we put a lot of work in, in the mid to late 1990s, to get bit level reproducibility - and even before that, those little details like timestamps were still deterministic variations, we had binary diff tools that could filter them out.)