“When that molecule has the same number of atoms, the same kinds of atoms, and the same structure, it is physically indistinguishable from any other identical molecule.”
Indistinguishable by our current level of understanding. There is far more to atomic structure than we can measure or even imagine.
I am a nuke engineer and did research for many years. Once you dig down, you see we are far from truly understanding anything.
I don't believe you.
Admittedly, education in STEM isn't what it used to be, but not ONE of the Engineers I ever taught would have come up with such a ridiculous statement. If you know anything about quantum mechanics (and based on your comments, you don't) you know that quantum mechanical particles are indistinguishable. That requirement applies to molecules. Two molecules that are have the same composition and the same structure are completely interchangeable: their vibrational, translational, rotational, intrinsic spin, and internal states are 100% identical.
There isn't any "new" science that's going to be discovered that's going to make it otherwise. The quantum statistical identity of quantum particles is so thoroughly established by so many experimental results (superfluid helium, properties of metals, quantum teleportation, the Exclusion Principle, ... I can go on for hours) that there's more likelihood that the Earth is flat than there is that what you're saying is true.