The problems are the same. You are communicating. This is what you do with software too. Organization charts are like architecture; take note of what supports the system and where it is weak.
The difference is that software crashes and throws errors. Humans try to fix their own problems when there's a bug. Sometimes this fix is not ideal to the rest of the system. You end up with things like one team pressuring another to extend a deadline, or buying excess junk to maximize their budget next year. You sometimes have to design the system to throw errors. Scrum is sort of like the managing equivalent of Java; it's bloated, slow, but it's safe and it works with dumb users.
There are lots of communication issues in every organization. You can do this manually or with tools, but you must be careful not to overengineer.
If you look, there's a lot more to refactor, and much of it is low hanging fruit. I'd suggest starting by tracking how the organization works and then trying to figure out how it can be optimized.
Flow state is reserved for creation/expression of large pieces of work. Manager work usually consists of smaller pieces and connecting them or making sure they work properly with lots of context switching. Can't flow there.