As usual, @pfaffman is quicker than I am, and knows his stuff. 
I never do upgrades from the GUI. That way every time I update, I will include any system security updates in the underlying containers on top of which Discourse is running. That’s saying it’s bad to use the GUI, nor is it a recommendation for everyone else. The GUI update have slightly lower downtime (restarting the web container does bip service momentarily, which one of several reasons to consider this together with external nginx) so it’s a trade-off, and I have taken the road less traveled.
A single-container installation has longer outages more often, if you regularly update for security updates as well as the occasional database version updates as Discourse takes advantage of new Postgresql features. Without reviewing actual data, my gut feeling is that there’s a reason to rebuild that 3-4 times per year. If that amount of downtime is OK from your perspective, there’s not a lot of reason to take on the complexity of the 2-container deployment.