What we fail to understand is not the coding, but how the system was built. It seems like its not just a simple flag in the header needs to be altered, rather an entire object class or model that needs to be changed or redone to accept the que, and if that is the case we don't know how large this object is and how much it affects the system entirely.
The object model for party and the object model for queing into instances may have strict checks, and if the companion model is embedded into the party object you are going to run into a wide range of issues trying to que into instances.
What issues? I can only guess that the instance server will have a tough time holding onto your companion model in your party while your in another party. Essentially you are trying to run 2 party objects one with you and chocobo, and 1 with you and the instance dungeon.
That's my guess from my basic knowledge in coding C++/C#/Python/Ruby/ObjectC.