Abuse of notation is incredibly common in mathematics, there’s no conflict there.

The abuse would be if you think that percentages should always refer to portions of the whole. Not sure that’s correct, though.

I don't know that I'd use the term abuse, but the basic idea is that there are things called odds ratios (Bayes' theorem looks especially convenient with them!) as distinct from things called probabilities... The distinction is precisely this one, that probabilities are implicitly normalized to 100% total while odds you're supposed to sum everything together and divide.

And then the point is just that we typically condition people to treat percentages as probabilities rather than odds. So you would have said something like 50:33:1:0.3 in “odds speak” for flour:water:salt:yeast in the dough mixture discussed in OP. But bakers instead communicate “:66:2:0.6” with the first number always implicitly being 100 (great), and they then use the % symbol (slightly confusing).

Because they never say “flour: 100%” an unsuspecting novice might think that a 60% hydration dough is ~40% flour by mass, mix this together to form a 150%-hydration mixture, and wonder why the only thing that they can make with it is some sort of pancakes.

As in it goes against the designed usage (where total is 100%), but it still works.

The total ingredients being 170% can be found confusing initially. I'm glad the author provided more context and the example of a 500g flour recipe.