Tested on latest(as of now) 3.8 but it seems should also work on latest(as of now) 3.9
I added 1.txt code to my admin/settings/server.php, after the '// "sessionhandling" settingpage' section, just before '// "stats" settingpage'
As for the actual custom timeouts(the values are in seconds), I added 2.txt to my config.php
I'm still learning(little by little when I have free time) about Moodle so I couldn't figure out how to make this work inside a theme, or if it is possible. If you know please let me know, thanks.
Note: I understand modifying core files is frown upon but for my required personal use and the required use of a couple clients sometimes there is no alternative(or no documentation on how to override something), if you also have to do it, try to keep track of the changes so you can easily apply them again when updating(it is important to stay updated to stay safe), you can even automate the process so it's not very complicated to apply patches to updates, just do it on a thoughtful way so you won't end up with broken code.