What if the Jack DNA actually did in part give Tim the twitch reflexes and fighting abilities? Perhaps without ongoing infusions he lost some of that. I don’t have all the lines in front of me but many TPS Tim callouts were very very Jack-like (which I get was part of the point in TPS).
Timothy has always never liked the position he was in. He was always nervous around Moxxi in TPS, most his lines still line up to his character save “kill lines”.