I get what you’re saying, but the measurements are real. In some sense they are the truth.

In the article this refers to the finding that the quark is more complex than three valence quarks.

The measurements indicating that the three-quark-model is incomplete are overwhelmingly conclusive, so some degree of certainty in the language is warranted in my view.

It's a pop sci magazine, of course they use language like that. Actual academic papers are different.

Not sure what this has to do with the article, it just seems like a nitpick. What did science do to you?