Nice guide, few comments below

maybe console-tools does it for you but when running it directly as described you need to run cal-tool to see the menu
otherwise the default is to wait briefly for menu key press and then boot directly with no menu. best is probably to set the root device to ask:yourpreferredmenuitemid so it shows the menu but boots your preferred item automatically after countdown

it is OK to ignore dialogs that pop up, the OS tries to automount your card when it is not formatted yet. However you should not ignore i/o errors when cloning, some people had issues with cards giving errors when writing data. Full format with Panasonic SD formatter sometimes helped. After cloning or when you suspect data corruption it is good idea to run dmesg command and check kernel log for mmc device i/o error messages. When something is wrong there are tons of them for every data block system failed to read or write.