(I agree that you should be able to reset.)

That said, the initial Grand Company Chocobo is not the only companion you will get!

For one, you will be a getting a black chocobo chick for your veterans rewards. Which you can raise and spec in a totally different way.

From what I've seen posted on this topic, you will still have your other Companions available too. So there is potential to have all Companions of different types, each with one of the 3 trees maxed, as well as a hybrid chocobo (like the one you may be thinking you already messed up).

To be honest, even though the Rank 10 skills look nice, having the three Level 1 Skills unlocked is probably the most useful spec for soloing/questing at this stage of the game.