No, you haven't missed anything. At the time of OP's bail application the State put forward that OP was wearing his prostheses. However the police expert who did the scientific analysis on the bathroom door, Lt Colonel Vermeulen, was of the belief that OP was on his stumps. Hence the PT went with that opinion. Capt Mangena testified that his ballistics report was based on the fact that OP said he was on his stumps. However, he qualified this by saying it was possible he was wearing his prostheses.
Be that as it may, neither Vermeulen nor Mangena stated that it was impossible for him to have been wearing his prostheses. Obviously if they made a categorical statement that he was on his stumps that would have been the end of the matter. However my belief is based on the fact it was possible. I guess it boils down to what you personally believe happened that night, taking into account all the known facts, probabilities, lies etc., because no-one will ever really know precisely what happened.
I'm one of the believers that there was an argument that escalated over the course of the evening. OP is a person who displays many narcissistic qualities - is controlling, has a sense of self-importance, believes he is special, has a sense of entitlement, lacks empathy and is arrogant. He also has a very hot temper. Because of this, I can't believe he'd have an argument with Reeva while on his stumps with her towering over him. He'd want to assume a more dominant posture which would necessitate him wearing his legs. I can't for one moment believe that he'd allow himself to literally be talked down to by her.
Secondly, he's stated over and over again how he was terrified after he perceived that an intruder/s may have entered his home, but nevertheless proceeded towards the danger when he had the opportunity to ring the police himself, activate the alarm, unlock the bedroom door and escape, shout out to the person that he was armed or wait in the bedroom with his firearm for the person to appear. After Dr Versfeld's testimony today regarding OP's many problems on his stumps - he finds it's difficult to walk, let alone run, he relies on light to see where his legs are and his balance is worse in the dark, I'm totally convinced that he was not on his stumps that night. JMO