The mongod docs say of the --shutdown flag: "Used in control scripts, the --shutdown option cleanly and safely terminates the mongod process." Unfortunately, the control scripts that are provided with mongod do not use this product feature, but instead execute the platform-typical kill. Examples of such scripts are https://github.com/mongodb/mongo/blob/master/rpm/init.d-mongod and https://github.com/mongodb/mongo/blob/master/debian/init.d.

If the control scripts do not use --shutdown because kill -TERM is just as safe and clean, then either the --shutdown docs should say so or the --shutdown option should be removed altogether.