Agreed as full VMs (or Virtualized Desktops) architecturally give you virtually the same thing as physical PC.
Regarding getting your screen layout optimized, did you try renaming your windows with a tool like GUIPropView and then running a layout for each window by name via something like ShiftWindow? It testing mine were all pretty easy to get laid out correctly everytime and others were able to get it to remove the borders at the top of each client (I got it removed on 1 but didn't do for all of them in my testing).
What are you using to bring a desired window into focus via keypress?
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