Hi, I have come across duplicated queries on the order page when this plugin is activated (using pro version). Please fix the problem to reduce errors and backend speed. First thought was woocommerce making these queries but after investigating it should be your plugin. Check out the github: https://github.com/woocommerce/woocommerce/issues/25046
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.