I havn’t found a solution yet. But got the tip to run the counter just as part of the level while rendering and keep it out of the sequencer.
That does work. But the timing significantly drifts apart from the 30fps of the movie render queue. So I am now at the assumption that even if I was able to start the counter within the sequencer the Timeline node would probably have to be controlled by the framerate of the sequencer as well.
That makes it even more complicated.
So I am thinking about hard coding the counter with keyframes in sequencer now. Not flexible and surely not very elegant. So I am still thankful for any creative ideas.