For one, completely remove presence based unlock and start would be a good first move. They are inherently insecure, as they are much too easy to relay attack.

Next, alter fob controls to encrypt the communication with private/public keys tied to the specific car. This way, even if the fob communication is intercepted, the information is functionally impossible to reverse engineer.

Finally, implement two way communication. An initial handshake followed by the command. This would functionally remove any chance of a replay attack. Even if the handshake is recorded, the fob won’t send the command.

These three changes would essentially remove any chance of using a device like a flipper for entry. Yes, it would still technically be susceptible with a relay attack, but the chances are so slim as to be essentially impossible.