"To turn it on it's head" ... yep, for sure!
Maybe, once again, my 'logic' doesn't equate, but here is my understanding ... maintenance mode keeps students/teachers from logging in. With those users not on system (assuming they weren't already on the system), running crons that update/cleanup/etc. ... purge cache etc., would result in 'cleaner' or 'unobstructed' platform for updates or upgrades.
Turning cron completely on/off isn't a function of Moodle code ... that's outside of Moodle and done by a server daemon ... which has other jobs. Granted some of those jobs normally slated for once a day and in the wee hours of the AM ... which, really could be the same time I happen to be working on Moodle! :|
BTW, I too, have done what I'd call 'ultra lockout' by shutting down apache completely, then running php scripts from CLI which aren't supposed to require apache be running. Don't have any sort of web page however telling users what's going on ... which might lead to frantic emails from admins unless they were warned in advance and checked their email/calendar. :|
Anyhoo, my 'boo-boo' simple to fix in my bash shell script ... just moved the cron line above setting maintenance mode. Mission accomplished ... was curious however, thus the post.
Thanks for the response.