Whats the point of chocobo restrictions?

[atomicdeath]

So we cant take them into a dungeon with us, but we also cant que for a dungeon with them in party.

One or the other of those need to go.

[kyuven]

It's actually a known and acknowledged issue with the way the duty finder works. Chocobos count as party members but they don't count as players. They've mentioned they're trying to find a way to work around it, though, but I can imagine just testing it would be a nightmare.
The current system is a stopgap until they figure out an actual solution, which may be coming in 3.0 as they've mentioned they're reworking a few other systems for that too.