The lighting operator is working under the privileges of the Ground controller's licence. Usually both have the same plan. Any unusual ones are discussed over the intercom beforehand (usually) or by specifying the ATCO's chosen route on the RT. eg: "...follow the greens, via....."
It's a pain for us ATCOS too, especially as sometimes our plan and the lighting operator's may differ or misunderstood. We often get pilots complaining about stop bars not going down in time. It's normally because your route cannot be selected until the aircraft ahead of you has vacated your "block" (remember those?). Often a few seconds of patience or not taxing up the backside of the guy in frony will help.... but of couse, being human, sometimes we forget.
But remember, it's there for everybody's safety. The view from the tower at night is not great and the ground radar cannot always be relied upon. The lights effectively give you a route protected from other aircraft, especially when vacating runways.
PS: why are pilots afraid of going through taxiways with blue edgelights when the green centreline lights have been switched off due to work in progress?