Your comments

Would it be possible to apply the same permissions to files added via the "Download and unpack" feature? That would be great for websites you always install via a .zip (like WordPress). :)
Understood. So I have to add "server" directives in the /etc/nginx.custom.d/yourconfig.conf but the other "location" directives can stay in "Advanced > Custom configuration"? It that correct?
That's a file I need to create manually or there is a section of the website panel where I can put that code? Is it in "Content > Custom configuration"?
I think it's the classic behavior of a text editor. You have no open file until you create/open one. :) So I thought it was a bug. But I see what you mean by "what's the point of having no files in Notepad" and it could stay like this.
The bug is not fixed. Right now, when I try to close the last file Notepad creates a new empty file:
http://shrrr.it/wyikbn24hs_video.mp4
I apologize, I was wrong. It looks like the plugin didn't overwrite my files.
The configuration is still in place and the error was somewhere else.

I should have checked twice before writing. :P
Okay it's not "create root". ;)

Anyway, that's what I do all the time but group is root and user is www-data. And I'm not able to quickly edit files via SFTP using my own account (which has sudo access, but I can't use sudo in the SFTP client). Is there a way to change that?
Where is that "create root" button?
Glad to know you still monitor this issue.
Enjoy your vacation. ;)