Krauss et al's statements on philosophy are simply that when you build a particle accelerator, walk into a lab, or start working out mathematical theories, you don't start with philosophy of science. That's a backwards rationalization of how science is done, constructing it's underpinnings/justification after the fact. Most scientists who conducted experiments and proposed hypotheses throughout history did not start by first making sure what they were doing aligned with the Philosophy of Science. And indeed, children conduct scientific investigations all the time blissfully unaware of the philosophical underpinnings justifying it.
I'll go one further and say that the idea that you never need to do "what if" theories, but merely explore the existing ones to their ends, can lead to local optima. It is certainly possible you will run into the limits of the conceptual underpinning of the theory in which no iterative refinement can fix it in a way that leads to superior understanding.
Philosophy is useful, in the same way that logic and mathematics are useful, to explore formal systems, especially when the real world experiments are impossible or unethical to conduct. But the limits of philosophy are also born out in the assumptions used -- e.g. arguments about free will or consciousness, debates are artificial definitions that do not measurably or provably reflect the real nature of real things.
Perhaps a better commentary here: http://whyevolutionistrue.wordpress.com/2014/08/23/accommoda...