reboot and shutdown time can be bypassed. In older retropie versions it rebooted / shutted down immediatly not saving the gamelists file, so any changes to them (like playcount, meta data from scraper etc) are not saved. They changed this to wait for emulation station to save all gamelists.
but you can easily get the original behaviour without waiting for emulationstation to shutdown and thus not saving the gamelists by adding 2 .sh scripts in the ports folder. in one you set the command sudo poweroff in the other sudo reboot along with the bin/sh or was it bin/bash stuff (have a look at one of the other files in the ports rom folder it’s normally the 1st line i’m talking about)
that’s what i do to reboot / shutdown my system immediatly and whenever i do want gamelists to be saved for example if i ever edit metdata data i just using the normal quiting way using start -> quit otherwise i go to the ports sections and select either one of those scripts