It’s a common workflow. The user wants to rename a reference designator, but doesn’t want to loose the link between Schematic<>PCB. The Netlist Importer has an option to “Link footprints using timestamps (Unique ID)”. But the Update Footprints from Schematic dialog does not have this option. I am requesting the addition of this option in the Update Footprints from Schematic Dialog box, which would allow the user to rename the item in the Schematic and sync those changes to the footprint more easily than creating a netlist and importing it that way.
I have never seen (or don’t remember) this first dialog box, but it looks that two radio-buttons from first dialog box were simply replaced with one check-box in second dialog box. If you switch off linking by reference than only one way left is to link by timestamp.
It’s the netlist importer dialog which should be revised, not the Update PCB from Schematic dialog. The latter’s UI was enhanced at some point, but the netlist import function is so rarely needed that apparently it was neglected.