1. What makes you think that the autobattle will fight better than a human? Just because you heard the word "chess"?
2. If the autobattle is used more often, as you say, and the losses are really acceptable, how will this prolong the game in real time? Do you use the autobattle when you have 2 angels against a horde of boars? Or not? This is actually a plus, as it will leave more time to think about the global strategy and the game itself, especially in PvP.
And there will be. To develop skill, you need something to practice on, but how will you learn when you are being practiced on?! Perhaps, for "farming," you could create a separate, more advanced logic for those who are really bored – that would be a good idea. But not more than that.