It is not possible to use https://roots.io/bedrock/ or similar frameworks which more accurately separate site specific code and content from wordpress core code because WPEngine assumes all the files of the site should be at the webroot of the site. Please give us a configuration option to set which folder in our project is the entrypoint of nginx, with the default being the project root (and therefore fully backward compatible).

The largest snag I foresee is this will make adding additional WP MU plugins trickier to install since the location of the MU folder could be anywhere in a framework of this nature. That should be resolvable by requiring a path to the MU folder setting that must be set when using a non-standard WordPress deployment pattern.