is there a specific reason https://github.com/PrefectHQ/prefect/pull/5729 wasn't merged yet? It only changes a few lines of code and helps anyone who has only access to custom S3 endpoints.

The main reason is that we are still working on some changes to the storage interface. Rather than using default storage, you will be able to customize it on a pre-deployment level with file systems It might be easier if we keep the discussion about it on GitHub since there's already an issue for it and once released, you can get notified if you subscribe to this topic https://discourse.prefect.io/tag/release-notes

Ah so that is the reason

Not sure whether specifying a custom endpoint would be part of that, but there will no longer be a concept of default storage - instead, you can specify that per deployment https://github.com/PrefectHQ/prefect/blob/orion/src/prefect/filesystems.py#L83 for using minio, check out https://github.com/tekumara/orion-demo