Alright I'll take the first two paragraphs of the capabilities you don't need to read it I'll reference it with a slight quote/paraphrase.

The user possesses all forms of science, powers, and potential, ascending themselves beyond superhuman, planetary, and mundane scale, achieving a potent scientific variation of nigh-omnipotence. The user naturally can manipulate matter, energy, forces, and particles on a microscopic and macroscopic scale, from operating on a subatomic scale or galactic size. They can affect the upscale structures of any material that exists in the universe and beyond; however, the user only has the potential to accomplish God-like features, not the information to execute them skillfully.

The user needs to understand their target, for example, molecules; the user needs to study extensively, read journals, books, notes, observe videos, photos, audio, or through supernatural means, like psychically absorbing physics-level intelligence. The second and final step is experimenting and learning new practices throughout their quas-physical journey. With this mindset and habits adopted into the user, they can further their arsenal and pouch of abilities, evolving to become an intelligent, resourceful, and intimidating scientific organism of raw scientific forces. The boundaries of the user's power can continue to convert into thinner layers, superseding their antagonists, peers, and limitations. The user can reach a level they can manipulate or redefine reality.

Ok the important bit lies in the fact that the first paragraph states the user possesses all forms of science, potential and powers (science related) that would mean they have Science Mastery. Now with that they have an understanding of all fields of science whether it be maths, physics or biology. The next paragraph says they need to understand their target so while things that exist outside of science will need to be observed and studied, they would be perfectly capable of controlling anything that is understood by science such as molecules due to their mastery over Chemistry or Molecular Physics. So that example while just an example doesn't actually fit. I really love that aspect of needing to understand whatever they want to control but when the power inherently gives you an understanding of pretty much all phenomena it kinda makes that aspect redundant.

tldr: Basically, the users possess all science powers including Science Mastery and they can manipulate anything they understand so they can manipulate any phenomena understood by science so that second paragraph is scuffed. I'd say it fits better for something like Super Science where they have Science-based powers and so having that scientific understanding will allow them to control that thing. It doesn't automatically include Science Mastery as it's just science-based powers. My guess is that Super Science falls under the levels for Science Mastery because it's a form/field of science and so someone with Science Mastery would eventually be able to understand it due to its scientific nature however it doesn't innately include all known science it's simply a field of it like Physics or Chemistry except it can sometimes control Physics and Chemistry or at least reproduce their phenomena through understanding.

Physical Godhood is essentially a combination of Science Mastery, Super Science and Meta Science (Basically Science Manipulation with guaranteed Science Mastery). The knowledge aspect of Science Mastery and the limitless influence of Super Science as well as the properties of Meta Science to change both Science Mastery and Super Science by changing the causal rules they follow.