Single app mode is the primary reason you're seeing this for a VPP app. The app can't update because it's open and can't close itself because the iPad can't go back to the spring board. We use a visitor management app on iPads throughout our campus and I regularly take these out of single app mode after-hours to allow the app to update. It's less of a process with Jamf School, but I did the same exact thing in Jamf Pro as well.
Technically we arent using Single App Mode or any MDM based Kiosk mode right now. We are simply launching a conference room kiosk app (Teem EventBoard) and activating Guided Access.
I think for now I will just set all the devices manually to not update App Store/VPP apps. Once I migrate them to Jamf Pro Ill experiment with other options.