A few thoughts.
Lift = a force acting at 90 degrees to the relative airflow. By definition, of course there is lift in autorotation.
If it wasn't POSSIBLE to complete an EOL without using collective every autogyro/gyrocopter flight would be it's first and last. I've done a collective-free EOL in a Whirlwind 10 but you DO need a good undercarriage (the groundcrew afterwards checked it and confirmed the Whirlwind u/c is a good one).
The key to how well a rotor system works is related to the amount of induced (downwards) flow. More induced flow = lower angle of attack = lower rotor efficiency.
Flare effect changes the direction of the relative airflow and reduces the induced flow, resulting in a reduced demand for power whilst increasing the angle of attack. It is, of course, a transitory effect that is taken advantage of during the penultimate stage of an EOL. The last stage is normally the application of collective to gain effective rotor thrust at the expense of Nr.
As far as the original question goes, YES there probably is some ground effect at the bottom of an EOL but as the aircraft is in ground effect suddenly and briefly, the effect is unnoticeable or hidden.