It’s better to run the last rsync with the --delete option when the node is stopped. It should take much less time, than the first two runs. It will update databases and should also remove all removed files to do not wait when the Garbage Collector would remove them, plus, it will fix partially copied databases.
For me - win-win.
If you would like to move nodes quickly - use either dd or analogue or LVM:
or ZFS send/receive.
For Windows there only cloning partition I believe. Which can be done with a Linux GPart from the Live USB stick.