The reason you see this message is because Total Upkeep does alter the auto-update system. WordPress detects this as a possible problem, but this is actually by design.
One of the features of Total Upkeep is to make sure that you have a backup of your site before a plugin, theme, or core auto-update. You can find the settings in Total Upkeep > Settings > Auto Updates.
If you do decide to upgrade to Total Upkeep Premium, there is an additional feature that allows you to wait a certain amount of time after a plugin or theme releases an update before the auto-upgrade. This can prevent you from installing an update that had a bug in it by allowing the developers to release more updates to fix any issues.
But, WordPress Site Health still sees this as a possible problem, and lets you know about it. As long as you’ve configured your Total Upkeep auto update settings the way you like them, you can safely ignore the warning.