Your understanding is close to the truth.
As far as I understand, "atomicity" in this context is a concept that was born way before the TON blockchain. It has probably emerged in the database field: https://en.wikipedia.org/wiki/Atomicity_(database_systems)
It uses the atom metaphor as something that can't be divided (even though humanity managed to split the atom after all). So the "atomic event" is an "undivisible" event. It may consist of several parts, but they act as a whole, they can't be separated.
What that means in practice is that if an atomic event starts to happen and some part of it happens, but then something prevents the next part from happening, than the first part gets rolled back. So the atomic event either happens completely or doesn't happen at all (since everything gets rolled back and returns to the initial state). It can't "half-happen".