global_mongodb_conf only gets the config file information for mongod processes that being run manually. It only looks for two file names, /etc/mongodb.conf and /etc/mongod.conf, and does not look for any files that are owned by an Automation Agent.
This can solved by adding one line and modifying one other. This is on line 228 of mdiag.sh:
automation_conf=`ps aux | awk '/automation-mongod.conf/ && !/awk/ { print $NF}'`
section global_mongodb_conf getfiles /etc/mongodb.conf /etc/mongod.conf $automation_conf
I've tested this locally and it works fine on Ubuntu Linux, even on hosts running multiple mongod processes with automation.