I resolved it by restoring my phone. was a pain though
Did a manual update to the iOS 12 Developer Beta 5 through iTunes using the IPSW file and it seemed to fix the App Store updates that were being problematic. The Software Update screen looks correct now too with the "Automatic Updates" option visible again (wasn't when "Cannot check for update" error was there). Not ideal, but can move back to Public Beta when v5 comes out.