Studio One's scenes are currently (up to 3.3.4) for track or console channel visibility only, they do not include automation or any other channel parameters or settings like gain, pan, etc. That may change in a later version, or not. But sure, you can use automation to automate settings, but they're not technically scenes, just automation changes at different parts of a mix.
With Studio One 3 Professional's Scratch Pad feature you can however write different automation setups in the same section by saving each different setup to a new Scratch Pad. Switching them will be manual, dragging a Scratch Pad back into arrange to "recall" one particular collection of settings or automation changes back for a given song section.