Yes, the boss battle was supposed to be that way as it was part of the twist for the ending.
And I agree that this system has potential for a lot more that can be done with it, I was even thinking to myself how I don't want it to fade out in the long run. We currently have no plans on expanding on this game outside of some minor additions, but perhaps we'll come back to it - if not using this system in another game.
Glad you enjoyed it and thanks for posting your score!