Yup, if someone is simply applying the scientific method without truly understanding its theoretical underpinnings, what are they really doing?

It's like driving a car with no mechanical knowledge. Not impossible, but if something goes wrong with the internal structures of it then you won't be able to figure out the problem and fix it on your own without seeking the help of someone who understands it.

And to be honest, I've seen a lot of dogmatic assertions from self-proclaimed atheists who view themselves as scientifically-minded while having no understanding of the philosophy of science.

Empiricism is great for what it's good for, but it's limited to observable phenomena. And without rationalism, it's like having a bunch of pieces of a puzzle and being unable to fit them together.

Here's a fact, here's another fact, and here's a third fact, but whether we realize it or not, we can't construct those facts into a coherent argument which leads to an accurate conclusion without utilizing rational processes. It's like focusing on factual soundness without paying any mind to logical validity.

And I see so many scientists making logical leaps that are quite simply invalid or fallacious. The most common one I see is "There's not enough evidence to support this hypothesis, therefore it must be untrue." It commits the fallacy of negating the antecedent.

If there's sufficient evidence, then the hypothesis must be true.

There is not sufficient evidence.

~~Therefore, the hypothesis isn't true.~~

It does not follow that the hypothesis isn't true.