I've used Maintenance Mode a lot for site upgrades and never had any trouble. It looks like that warning relates to the slightly challenging requirement for Moodle to restrict access to items that there's not normally access control for.
Best practice in my opinion: climaintenance.html in your Moodledata folder. This page will be shown to anyone trying to access the site but this includes admins too. So it's great if you're happy upgrading the site using the command line but maybe doesn't fulfil the non-technical requirement.
It also depends how large your site is: the larger the site the longer the upgrade takes, the longer the upgrade takes the more chance of users attempting access. Hopefully you'll have some idea of how long it will take from performing a test upgrade (which is highly recommended).
There's a plugin, Outage Manager, which allows you to restrict access to only specified IP addresses which may help. I haven't used it so I can't give you any insight I'm afraid.