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.
Percentages are just a way of writing rational numbers. Bread recipes are expressed effectively as 1 part flour to n parts of each ingredient. But since n in that formulation is usually a value less than 1, expressing that number as a percentage is convenient. Percentage notation seems completely appropriate for this usecase.
So 60% hydration means 1 part flour to 60% of 1 part water, i.e. to .6 parts water.
The abuse would be if you think that percentages should always refer to portions of the whole. Not sure that’s correct, though.