This is where you bury the lede. It's clear if you read many of the comments here that there is no such agreement. Some people _think_ of an atom as something you can reach out and touch, or grok in some deep sense distinct from performing specific experiments. Others take an approach that's more in line with theory in the sense I use it (https://en.wikipedia.org/wiki/Scientific_theory). Your definition of theory is too loose: it's not just a body of work. That sounds like a pile of experimental evidence to me. A theory is a robust model or family of related models that match the experimental evidence. Atoms exist in that sense: they're a well tested model of experimental phenomena.
I'm certainly not claiming that atomic theory is a wild speculative guess which you seem to imply I've done.