I guess I don't understand how it works. I assume the main office sends qualified people to places they see a need. Why would someone open an unofficial house without approval? If they see a need somewhere why can't they request approval?
The official umbrella organization that "sends out" Shluchim is called Merkos L'Inyonei Chinuch. Merkos appointed "head shluchim" for various regions. Rabbi Cunin runs California, Rabbi Korf Florida, etc. They hire Shluchim for the various mosdos and cities within their region. Those Shluchim can in turn hire Shluchim to run even more local centers or programs/mosdos within that Chabad House. Shliach oseh Shliach... Decisions about policies and protocols are made at a local level with local Rabonim, or other Rabonim can be brought in if needed to help with disputes. Each Chabad center is locally funded. So if you go to a small Chabad House in California, they aren't getting funding from Merkos or Rabbi Cunin.
Why would someone open an unofficial Chabad House? Plenty of reasons. An existing Shliach gets into a dispute with their "head Shliach" and instead of leaving, continues operating just without being recognized. Or they just couldn't be bothered to go the official route and want to run their own thing. Maybe they want to open a new place in an underserved area but couldn't work things out and decided to go ahead with it anyway.
As for how this applies to this thread: there is no official policy or protocols set out by Merkos for Shluchim to follow for their catering/restaurants/Chabad Houses. So it wouldn't make a difference if the Chabad House was sanctioned or not, it is the same question of whether or not you trust the guy.