Your config file for
KataGo is not setting friendlyPassOk: false option, and therefore KataGo rules are not set to be Tromp-Taylor.
KataGo will perform "friendly early pass", which is what you report in your paper.
Tromp-Taylor configuration is prescribed here: https://github.com/lightvector/KataGo/blob/master/docs/GTP_Extensions.md
To summarize, your bot and you judging code is working with Tromp-Taylor rules while KataGo is not.
This misconfiguration is the root cause why your network is able to exploit KataGo.
I'm sorry that this invalidates the main result of your paper.
Notably there was a case where a human player exploited the rules in similar way.