A lot of this confusion has to do with the assumption that substance cannot be anything but atomic. Substance could easily have a number of other possible states (even parallel to the atomic).
Remember, "What is substance?" is not addressed by contemporary science, which (to it's credit) always deals with discrete objects or catagories of objects (what is a thing made of? Matter. What is matter "made of"? Atoms. What is an atom made? Sub-atomic particles. Of what are sub-atomic particles made? Eventually you have to say "this thing is best described by it's behaviour" (eg. wave functions)" in three+ dimensions...).
The reason substance is not addressed is that it is not that meaningful. Pure, non-atomic substance can only have a limited number of (easily deduced) properties, not including things like density, in the end leading to a circular or tautological conclusion: those properties unique to substance define it as such, meaning there is really only one substance possible and all matter is composed of that.
So it may seem irrelevent, but keep in mind all our current grand theories of reality depend on the actual existence of substance, which "actually existing" is a one of the properties unique to substance which define what it is (all actually existing things are derived from substance).
Part of the reason so many scientists are so interested in the big bang and the "first few seconds" today is that this is when the current laws of (nuclear, atomic) physics could and probably did develop (they did not have to exist "before" this, so we have a moment zero when the concept of time becomes applicable in the universe; hence there really may be parallel, non-atomic states of substance "outside of time").
If you don't believe that "substance" has always been a consideration (explicit or implicit) consider that the "atomic weight" of an element is really its physical size.