You're right, the current code is only rate-limiting the requests to this file.
For now, the only way is to modify the wpcommon.conf file, definitely we need to change it and allow users to have their own choice at least with this specific file, especially when it's a very common case like this. I will add this feature in our roadmap and maybe we will have a permanent solution released in v1.14.0.
Nginx configuration files are not always overwritten in each Webinoly update, just when the stack version is raised. Check: sudo webinoly -v
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