Right there with you. I resigned myself to working around the behaviour by setting up quick connect profiles with 5900, 5901, 5902, 5903, etc. It could take 2 or 3 tries to get the machine I want, but I eventually get there.
The overarching issue of GUI changes killing XML customizations is a VERY longstanding issue, apparently the intent was to wrap all possible changes into the GUI and only the most obscure changes should need to be made manually. But, as you point out, there are some really common tweaks that aren't in the GUI, like a working boot order changer, vnc settings, etc, etc.
Honestly I think the answer is to scrap the VM gui entirely and plug in an adaptation of virt-manager.