If this story were to remove the isekai aspect entirely, she could just have said that she was gifted from birth to be able to control "the sands that construct all of our reality" and make some cool worldbuilding effort to explain atoms and molecules that we know of using their fantasy knowledge.
But no, the author goes lazy and said "because isekai" for the sake of isekai.
I'm pretty sure molecular science goes deeper as well; two I can think of are molecular biology (which is incredibly vast) and material science. The author probably didn't do their homework and just want a cheap and easy reason to explain MC's cheat isekai skill. There isn't a "molecular scientist", jobs nowadays goes into more specific areas.
And by being a literal large hadron collider in which she's just able to combine atoms to produce anything she wants, it just removed all the interesting aspects of molecules. I go to a science college and all the chemical reactions, electron and group transfers and whatnot, they're all fascinating once you get the grasp of it. I'll give the author a benefit of the doubt and assume that they have zero clue about what I'm talking about cause they didn't learn it. This is fantasy - they could worldbuild on how MC's spirit power guides atoms to react on her will or just make up something up. They may be unaware, but they're breaking the "show, don't tell" rule of storytelling just by having the MC explain what molecules are.
Even Kenja no Mago who have a lower rating have better worldbuilding. There, the author actually explains how an explosion magic works by gathering all the oxygen and bla bla bla but here, the author decides "it's a cheat skill, I don't need to think about worldbuilding!"
It's just bad writing. Pretty sure that 6 out of the 8/10 rating on this manga comes from the cute loli alone.
K I'm done ranting.