I'm pretty sure we've done it before by creating a special permissions called Add Only, but is there any way to keep those Power Apps users from being able to navigate native SharePoint? In particular the root and list default home pages?
I think the best way is to not give those users any access to that site. Manually create a connection that uses a dedicated user account that DOES have access to that site and destination list. Then your App essentially has access to the site, but your end users do not.