My workflow is almost a match of CWN's (I don't do the Last Item).
I tries setting my Calibre up leaning towards modal use.
Menubar has Preferences, Help, Fetch News,
The Main Menu is Library/Device oriented
The Second toolbar is Book Oriented
Having a configuration export/import tool that would log the dependencies (and maybe package them as well) and export the exact configuration (settings, Column coloring rules...)
Import would do the reverse (and warn if there were User (PI) Items that would be removed)