My score count is strictly related to the special rule: every enemy counts 1. You have to defeat the last boss twice, in different conditions, so i think he should give you 2 points.
To make things more interesting, i suggest to count points only for enemies that are defeated in normal combat situations (no QTE). This is also necessary in a couple of times to obtain the maximum possible points

I think that's not a good idea to give points for the three enemies beaten via QTE at the end of the last stage, because you have to finish them in normal combat anyway and the "success" only gives you the advantage of starting the battle with every enemy down and unarmed.