Preventing WordPress from being put into maintenance mode

I found your plugin organizer on a WP Engine article as their recommended option for selectively loading plugins. The plugin though interferes with WPE’s Smart Plugin Manager which automatically updates plugins, checks for issues, and then rolls back updates if something is broken. WPE support looked and something with plugin organizer may be preventing WordPress from being put into maintenance mode for some reason. Specifically they saw it was returning a 200 response instead of 503 as expected when a .maintenance file is added. Is there a setting or something we are missing? I looked at the FAQ and documentation and didn’t see anything regarding maintenance mode.