Molecular geometry, also known as the molecular structure, is the three-dimensional structure or arrangement of atoms in a molecule. Understanding the molecular structure of a compound can help determine the polarity, reactivity, phase of matter, color, magnetism, as well as the biological activity.
Changing bone density and increasing blood flow to augment stimuli falls under a molecular change.
Zoros abilities does not come from a something artificial or something not his own. Hence why using hakinor weapons does not constitute as a base or transformation. It's the same with sanji Germa Gene's.
No sanji using a raid suit would be a transformation and thus not a base form.
A zoan transformation would also be a transformation.
Luffy again changing his body structure to use attacks he can't ordinarily use does not fall under the parameter of base form
Using the lens of chemistry to talk about what are essentially magical-biological phenomena is a bit strange and awkward.
Simply streteching his arms would create a "molecular change" of the state of his arms because of the increase in elastic potential energy (and ignoring the laws of conservation of mass among other things leading to some implications).
Soru is a martial art technique, G2 is the application of that technique on a rubberized body.
G3 are individual attacks with no backlash or cooldown, they are no longer a mode Luffy needs to stay in to chain attacks before shrinking.
Calling haki "natural" is a bit strange, when it is a supernatural force.
Swords aren't "natural" or inherent either, they are external tools, especially meito that defy physics with their natural durability, especially meito like Enma that have supernatural effects. Meito can be taken from Zoro far easier than Luffy's fruit can be taken from him.
Genetic modification isn't "natural".
The crux of the issue is not "naturality" of a certain ability if we are talking about hypothetical matchups, but if that ability can be stripped from you in an in-universe means to create a scenario where you don't have that ability, for the purpose of seeing how a certain character would fair in such a situation. These are powerscaling terms of effort/difficulty, not philosophical discussions about the naturality.