I don’t think it’s possible to extract FlowCanvas to work outside of Unity without some heavy source code changes, since there are some tight dependencies with UnityEngine like you said. By the way, a FlowScript is a ScriptableObject, so basically it is wrapped in a ScriptableObject rather than a MonoBehaviour. The FlowScriptController component is just a convenience way of using a FlowScript. I suppose though you would even want to split the dependency from ScriptableObject as well, since that’s a UnityEngine class.
So, unfortunately I can’t think of a easy way to extract FlowCanvas and make it work completely outside of Unity at this point. :/