You're right, although the F relay is labeled "00-90" relay it's driven by the L or 1000 point relay. It doesn't change every time 1000 points are scored though:
Top Card F relay (resized).jpg
During reset it is driven by pulses from the Score Motor 1A switch through another switch on the A/Reset relay for as long as reset takes. But during game play it is driven by the L/1000 point relay through the same Runout switch used to reset the 1000 point score reel. That means that the F relay fires and the pop bumper lights change when 1000 points are scored (L/1000 point relay fires) and the score reel isn't showing 0 (when the Runout switch is open).
I hadn't seen this before but it's another way to randomize the match calculation which is also driven by the F relay.