I've seen this exact thing happen with data infrastructure. Teams build this pristine lakehouse docs site, standardize on dbt, create "golden path" templates. Then someone needs to join a dataset that doesn't fit the pattern and they're stuck because the portal enforces one way of thinking.
What actually worked: stop optimizing for discoverability first. Start with making the exceptions easy. Build your docs around real problems people hit, not ideal workflows. And critically, make it trivial to do things outside the system when needed. You lose some consistency but you unblock people fast.