The fact that she was trained by MHX is actually very important since MHX is pretty skilled, and didn't that ttaining ended in she having a skill or NP upgrade? And yes, that scene is bwfore she trained with MHX, it was at the beginning of Saber Wars I.
And as said before, she don't have anything that make her special, not mention of anything that could let her detect that in her skills, NP or materials, at most maybe could be argumented that it was her Instincts? But her Instincts don't have a need to activate because said things can't kill or damage her body, also, if she knew about that do to her Instincts she would had say so, something like 'It's fine, my instincts tell me there is no danger like radiation, killer viruses or other microscopics dangers', actually they way she worded it make it seem like it's something so common that even she despite her lack of experience can detect.
Similarly Medusa don't hace anything special regarding that, her strength skill don't mention that she can do that do to it, her Mystic Eyes also don't mention something similar and in the scene they even are sealed do to the glasses, the other most special thing she have is her divinity, but there is no mention of things like that in the skill and would be needed a lot of assumptions that is do to divinity that she can do that. The fact that other sevants constantly interact with spirit origins support that that is something everyone can do.
I understand the motive of wanting to classify this as things exclusive to Lily and Medusa, but do to the lack of reason about why they would be the only ones able to do said things and the amount of assumptions needed with that I just can't see it as something unique to them and instead as a trait that every servant have.