Hi Kevin,
I had a look at the duplicate queries mentioned in the issue link you specified and those are as a result of fetching Shipping methods and zones.
If you do not have a use case where you would want to restrict the custom payment gateways for specific shipping method or zone then I would recommend you to disable the “Shipping methods” under the “Advanced Options” here: https://www.screencast.com/t/6OlUgFgg
I am working on creating a fix where the Shipping methods would be cached to avoid duplicate queries.
Please let me know if there are any improvements after disabling the above setting. After disabling the setting, I was not able to find any duplicate queries.
Thanks,
Dhruvin