I'm sure you guys are aware of http://php.net/manual/en/function.set-time-limit.php
Well, anyways. The CLI did do all the migrations overnight.
Maybe the problem lies in the documentation, where one cannot find any discalimers that if one is running a forum with database size of over, say 1 GB (or whatever), please update files with installer and then use phpbbcli to migrate the database.
I also wasn't happy that the updater requires PATH_INFO (app.php/upgrade or whatever the path was) where as the site otherwise won't use PATH_INFO. Had to temporarily update nginx config to allow this.
Also updated my PHP-FPM docker container to run PHP 7.1 and request times were basically cut in half. Yay