I think you're right, once I started doing burns like in KSP1 my orbits would align more with the predicted trajectory from the burn timer. The burn timer is a nice idea but I dont think its working at the moment. for example: limiting the thrust on your main engine doesnt affect the burn timer at all so I stopped using it altogether :').
I don't think it has to do with the dots turning green too early. It's probably as larsonco said, the burn countdown should start before the actual node, not when it's on the node exactly. Then again I have no clue if this is intended and if it's only happening to me.
