Not sure I agree with the conclusion of that article, according to it, only 2 screen readers don't support nested labels, I couldn't find statistics on how prevalent these are, but there are a lot of alternative screen readers one could use which might support nested labels since they're not mentioned there (I've mainly heard of JAWS, which isn't mentioned there), so it doesn't seem to be an inherent limitation of assistive technology, just a bug in some (popular?) screen readers.
VoiceControl and Naturally Speaking aren’t screen readers: they’re voice command software. They’re designed for people with mobility problems, not vision problems. There’s no inherent limitation here that couldn’t be solved by bug fixes, but they’re the two major pieces of assistive tech in that sector so can’t be dismissed without dismissing people who need that functionality.
Fair enough, so to test things out I've enabled Voice Control and tried whether it makes a difference how the elements were arranged:
At least with Chrome, it does not make a difference! It correctly determined the label and I could just tell it to click on that particular checkbox.
Since Dragon Naturally Speaking doesn't seem to have a trial, as well as having a broken shop page you can't order from, I can't give it a test, but that articles advice seems rather questionable to me.