That is a beige flag at worst. Every organisation has unwritten power structures that (often) exclude newcomers. Some organisations also have additional written power structures that (often) exclude newcomers.
While you're correct, my experience has been that the unwritten power structure is much stronger in places where there is no written power structure.
Where there is a written power structure you can usually appeal to it and eventually get something done. Where there exists no written power structure at all, you're out of luck unless you can quickly figure out what the power structure is.
A written power structure is a low resolution map. It's not perfect, but it gives you some idea of where to start making sense of things. A flat organization is never actually flat, but it also has no guideposts at all to show you even the rough outlines of the real hierarchies.
I worked in an organization with a low written structure. Creating unwritten structure is necessary consequence - each it happened as a reaction on serious dysfunction. And each time it improved things. And what you learned each time is that if you dont keep power, things will get very bad again.
Imo, that is argument for written structure. Written structure is easier to talk about openly talk about, reason about and fix. Unwritten structure is inferior consequence of its lack.
This is analogous to the 'unlimited' vacation policy. Now instead of following a codified and shared standard the employee has to negotiate every vacation day and consider how it impacts their standing in the organization.
