Hey @Stuurlui
MainWP always starts with the sites whose last automatic update check began the longest time ago (including any that have never been checked).
Each minute during your cron window it pulls up to four of those “oldest” sites, kicks off their update checks, then records the current time so they fall to the back of the line. The next minute it again takes the sites now longest-waiting.
So the order is basically “oldest last-update-check first.”