The way to configure "Prompt and Countdown For" properly in reboot maintenance window settings is over-complicated, partner is hoping for this to be more simple to understand(current design is very complex and not having enough explanations in online help documentation).
This is how it actually works(makes sense but not intuitive based on the UI design):
"Prompt and Countdown For:" should be the same number or smaller than the "Maintenance Window Should Last For:" for them to work together the best.
"Prompt and Countdown For:" controls how much time it prompts for, if no user is logged in that device, it will not prompt(this time being configured will be useless), if a user is logged in but locked screen, than it will prompt for that much time and try to reboot;
"Maintenance Window Should Last For:" controls for how much time the device is allowed to reboot, so when the prompt timer eventually finishes counting down and try to reboot, if it's already outside of the window of "Maintenance Window Should Last For:" then this reboot request will be ignored.