That's it exactly....no evidence. They (the State & police) can have all the suspicions in the world about what caused XYZ, but without actual evidence, they have nothing to contradict whatever explanation OP chooses to give.
I think, regarding the bullet hole in the bedroom door, if there was scientific evidence that the hole was "fresh", this would have been close to impossible for OP to fit innocently into his "version" and Nel would have raised it.
I can only assume that they were not able to conclusively say how old it was.
His explanation for the bashed in bedroom door was bloody ridiculous. He wanted to open it, so ran into it....then bent down to unlatch it???? Round object.
And the dented bath panel was raised by Vermeulen....he couldn't determine what had caused it, but had found traces of copper. So if OP said, "It happened when I pulled the plank out of the door and flung it down", then that's the end of that. He can't be contradicted.
Having said all that, I think the State could have done a far, far better job of nailing down some specifics. An alternative timeline for Masipa to consider might have helped. Or not. But not even to mention it seems incredible to me.
Also have to assume that whatever food scraps were found in the kitchen did not contradict OP. Of course, this can only say what was eaten, not when....so totally irrelevant, so not surprised they didn't bother with that.