FlowStudio has been more or less dormant for a few years already and I don't have any plans to resume work for the time being (but who knows, one day maybe I regain some motivation). As to your question, there are many things that could be improved or be implemented differently as regards projects but the current implementation at least fitted my own way of working. Note that it is already now possible to have multiple "Projects" in a single "Work Space". These projects will all show up in the tree view. The distinction between sources, headers and resources is one step down in the hierarchy.

As far as I remember, there is also a way to link those projects in a single build but this might be an area where further work would be needed to fit all needs.