Interesting theory, but I don't think that's quite the case
at the beginning we were controlling our host bot BEFORE ever running into Chatot, then there's the fact that that when we encountered Chatot it was "Oak" that caught it and was going to give it to our rival (before he stole the starter we were JUST about to grab for himself) only giving us the Chatot cos the pokemon he was going to give to us had already been taken, and it was told to us that Chatot did'nt seem to like our host when we got him...
I think all that together points to the bot being our host
HOWEVER, we did'nt reely start noticing some of the bigger oddity's of this game until after we got chatot (such as the emote interface and some of the odd dialogue) so I think it's obvious that chatot is more then just a regular mon.
what I think is that the bot is out host, BUT our host bot is somewhat defective, Chatot seems to be picking up on this somehow and is able to head and transcribe what we (as the voices) are saying to out host and as such wile the bot is our host the chatot is just as important (if not maybe slightly more so)