A very simple solution to this will be to use weight sensors like cars (the sensors car use to determine if there is a front seat passenger and turn on airbag). If those are installed on 15k usd cars they cant be expensive either.
Using these with some software to alert the crew if more than expected seats are in use in any cabin >=PE.
Another potential approach is to make a record of passengers who are self upgrading (BPs have seat numbers which have enough information to track them). Something like warning for the first 2 times and then put them on Nofly list for the airline until they have paid the difference between the cabins.