I don't think there's a contradiction. Modern philosophy never claimed to be science, while modern Theoretical Physics (science) in many parts strongly resembles philosophy, as you said, while never acknowledging it. Theoretical Physics is supposed to be a complement to Experimental Physics, explaining or predicting things that could later be confirmed by the Experimental branch.

I think string theory as a theory of everything is an excellent example. From the outside at first it seemed promising, but nowadays looks more like a very complex mathematical chimera which we don't have a particular way of proving nor disproving. But string theorists insist that these aren't merely thought experiments, this is SCIENCE, even if we have to add dimensions and multiple universes we never experimentally detected to try to make it work. Maybe it works in a blackboard, ¿but how do we know it reflects reality?

Philosophy of Science should be useful to check if we are doing science right or are being carried away by beautiful math and thought experiments. Maybe a scientist doesn't need philosophy a priori to do science, as a doctor doesn't need philosophy to cure people, but both epistemology and ethics are useful to contemplate if we are doing it right or something should be improved. At least that's my opinion.