Timeout in sites, perhaps related to cron
Even if you say its not: This issue is most commonly not only Drupal 8 related. You will find issues for Drupal 7 reporting near the same behaviour. It turns out that cron starts after the expired period with first page request. If this happens, the cron seems to take endless time and seems to interfere with the page request in the same moment. Many experienced users run their crons from Drush manually or combine it with server crons. But generally spoken :

There are 3 possible points to look at and to modify (and you already named some of them), which all can interfere each other or can be responsible for it each at their own allone:


Take a look at your php and apache settings for memory, cache size
and sql query time settings. Cron is a big wave coming. From my
experience a smooth Drupal experience can be only granted by
increasing it over the given amount suggested.
Turn off automatic cron frequence (as you sad, mostly set by 3
hours, set it to -none-) in the admin/config pages, but make sure
that you run cron by yourself manually often enough (thats how I
generally do it). For some reasons and some unclear circumstances
(mostly server related) this is often the only option to prevent
this behaviour.
Make sure that you have turned off all unneeded modules on
production sites. Even if some suggestions say its not related, my
experience is, that turning off help, update, dblog (use syslog
instead) etc. at production sites makes Drupal faster and prevents
such overheats.