Chat.Meta.SE has a different purpose than Chat.SE both of which are distinct from Chat.SO.
- The moderators on all 170 network sites (including Stack Overflow) have moderation tools available to them on the Chat.SE server.
- The moderators on Stack Overflow are the only moderators who have moderation tools available on the Chat.SO server.
- On the Chat.Meta.SE only staff (including the Community Managers) have moderation tools available and unlimited access to all rooms.
Where you're a moderator determines your ability to access certain rooms. Private rooms (moderator rooms) can only be accessed without special permissions if you are a moderator on the site/server the room exists on. Unparented private chat rooms (on the chat.SE server) can be accessed by all users with diamonds.
When it comes to Chat.Meta.SE, the staff use this separation to have super secret rooms where magic happens... mostly discussion of waffles, I assume. As you can see, this is confirmed by a Community Manager here:
Also of note that chat.meta has a bunch of internal, very active staff-only rooms that'd have to be migrated if that occurred. Merging them is not a particularly simple task only due to the appearance of it being less active. – animuson♦ Jun 17 '17 at 23:11
Though, despite my initial assumption that these rooms would be accessible to anyone with a diamond on the server, the reality is that staff have special access on their accounts that lets them get into these rooms. Merging wouldn't be impossible but it would be complicated and (my guess is that) there are more pressing things to handle.
In addition to these staff-only rooms, the CMs will occasionally use the Chat.Meta.SE server to have private conversations with users. Because the private rooms on the other two servers can be accessed by the site mods there, these rooms can't be completely "private", as the mods could find them at some point.
While rooms can be re-parented to other sites on the Chat.SE server under certain conditions (including SO and MSE), this isn't changing their server, which is impossible.
As to why it is this way, there was an intention at some point of creating a separate chat site for every network site. This was long ago:
To be honest, much of the "parent user" idea is still a leftover of the original plan to let each StackExchange site have its own chat site. You can see this in http://chat.meta.stackoverflow.com and http://chat.stackoverflow.com/ – having a "parent user" here obviously makes sense.
At some point, we decided that not every single SE site needs its own chat site; it's much nicer for the community to gather on http://chat.stackexchange.com. This was also in the very early days of expanding the Stack Exchange network via the Area 51 process. The very first SE 2.0 site (Web Apps) was launched around the same time as chat.
Note, "chat.meta.stackoverflow" is what we now call "Chat.Meta.SE". This was, as you can read, abandoned, instead favoring having a single chat server for all network sites other than Stack Overflow and Meta Stack Exchange.