Sorry for the delay. There is nothing suspicious here. If you are "running" the server process as the operating system user "joe", all the newly created files in that domain will assume "joe"'s permissions. This is the normal procedure. User "joe" "creates" a domain and "runs" it.
Now, it may so happen that you have more complicated setup where some you are running in a chroot-jail or doing seteuid etc. but under normal circumstances, GF is run by a user who creates its config folder.
-Kedar
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