Getting China Visa on Arrival when flying with a China airline which transits in a China city first

We have been refused check-in at Rome FCO airport on a flight with Hainan Airlines to Hainan today because the Rome FCO check-in representatives (and supervisors) insist that we need a china visa and that we cannot obtain a Hainan China visa on arrival.

The reason that gave is that the flight from Rome FCO transits at Chongqing airport (for a few hours) and therefore we will be entering another China city immediately before arrival in Haikou, which then disqualifies us from obtaining a Visa on Arrival at Haikou.

We have studied the rules very carefully, and we believe that the Rome agent has got it wrong - and that misunderstood the rules of the Hainan VOA.

Note that we booked the tickets directly with Hainan Airlines, not through a travel agent.

Can you please advise us.