In general, if you already have a volume control integration that is better than can be achieved via a harmony remote, then you should stick with your existing control. This is why there is an option to omit controls you don’t need.
If I understand what you are saying however, then are you are saying that Harmony cannot control the Atom (Ignoring my Roon extension for now) - ie Logitech have not provided a profile for it perhaps via wifi?
If the answer is that Harmony cannot directly control the atom, then a future option I had already in mind was to allow Harmony remote volume and mute to directly control Roon (rather then the current other way around where Roon controls a device via Harmony). This would then allow volume and mute buttons on Harmony to control devices that are already controlled by Roon (ie USB DACs, or any device that already has a more specific direct volume control extension available, for eg Yamaha and Denon AVRs).