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Workbench will be the colours saved on whatever floppy disk it's booted with, so if both machines were booted with the same 1.x Workbench disk, both will have a blue background regardless of Kickstart version.
I think starting with WinUAE is a very good idea, so you can get a handle on the capabilities and limitations of such a setup. The software and files can later be transferred to a real Amiga if you wish.
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