There can be many different web server settings and set ups. I propose have a "recommended" core server and wp-config.php set up that is made public (and can be a live document that get updated) that all WPMU developers and testers will first test against ( in addition testing would go on for other set ups)
Because @Sam is in charge of the most important wpmudev plugins, I think he would the lead on this live document.
This might help get more people on the same page and get everybody using best practices for server set ups.
At the very least it would be good to see the nginx files and wp-config files that the developers test against currently.