The onus for ensuring a rider is eligible to guest surely rests with the club engaging him. The referee gets a list of each team's line-up three days prior to a meeting, and checks to ensure their averages are correct, not if they are cup-tied, which is hardly his business.
If an ineligible rider somehow gets tracked (as with Drew Kemp at Scunny) it'll always be realised at some point, before, during or after the match, and -- if it really matters -- his points deducted and the result amended.
In this case, the points from his three races only marginally change the scoreline, Scunny still win on the night and on aggregate. Riders' averages aren't affected by a play-off meeting and we can all settle down.
Bad move by Scunny not to check on his eligibility tho. Might have cost them dearly!