I agree, I was supper confused when I realized it about a week ago.
I initially assumed Flowcharts controller hold their own data and state, just like a the JSON, Array and Dictionary Plugins. But it seems like flowchart controllers all reference the same current flowchart, they only differ in the state of that current flowchart.
This makes it way less flexible, can't really have one flowchartController for npc dialogue (maybe you would even want to have a flowchart controller in a container of each npc, each referencing their own dialogue tree) and one for the progression system etc.
With the current implementation it means you have to swap the flowchart all the time making it really weird imo.
Tough I'm sad as it seems like it might be too late to change it due to backwards compat.