The stumbling was all mine. For instance, when the device wasn't showing up, referring back to the docs about it being a combo box straightened me out. And my Platform Tools wasn't up to date which turned out to be dumb luck because replacing those files is when Magisk finally asked about granting root to shell. Stuff like that and having ducks in a row.
After a couple more updates with PixelFlasher I think it'll be second nature. As far as I can tell you've covered all bases and I have no ideas for improvements. The UI is neat and makes perfect sense after staring at it a while. Whether to flash both slots seems the only question for now but since the 13 bootloader is on both I haven't been concerned about that.