To elaborate further on how Thomistic concepts like substance, accident, potentiality, and actuality fit with modern science:
A-T philosophy analyzes concepts at the macro-, everyday level. They start from basic commonsense observations that individual persons seem to exist as a unity - I can point to my father over there and differentiate him from the chair he’s sitting in, other people around him, the floor, and the things he’s holding. Now, today we know that the human body is made of organic molecules. A naive modernist would simply say that my perception of my father as a separate entity is an illusion, a trick that my mind plays on me - there is no unified substance known as my father, only a collection of molecules acting together due to the laws of nature. The Aristotelian would object and say that that the perceived unity actually exists, that my father is actually one united substance. Neither side can evade the scientific fact that organic molecules exist in my father; rather, we are asking the question is there some objectively existing (i.e. extramental) higher-level principle that governs those molecules forming my father such that they accord with our commonsense observations?
In other words, A-T philosophy today is trying to analyze nature not by breaking it down into smaller constituents (which is what modern science does, most of the time), but by trying to deduce general, non-reductionist philosophical principles which govern reality in light of both commonsense experience and empirical evidence discovered by the tools of modern science.
It is true that some forms of A-T philosophy would require you to adopt an anti-realist view of science, such that atoms and molecules only exist virtually in some substances. But anti-realist views of science are common among many philosophers of science, not only Thomists. In fact, I think it would be rare to find a philosopher of science (or even a scientist) who would take a completely naive realist view to the objects science studies. (This is again, another topic on its own.) There are many people who take an extreme anti-realist view that the only things really existing are measurements - all our physical theories are just tentative models used to explain the facts we have. (This was my own view just a few years ago, completely unmotivated by any religious or philosophical considerations.) In fact, Thomists such as Edward Feser take a stronger structural realist view to science where they think scientific theories reflect real structures found in nature.
It would be inane to accuse everyone who is not a naive realist in their philosophy of science to be dabbling in pseudoscience. Such an accusation betrays a lack of understanding of what philosophy is and what it is useful for.