The section on iTunes Media Organization is relevant here. Consolidate Files only affects content outside the currently designated media folder. Turning Keep organized off, applying, then turning it back on, rearranges what is inside the media folder according to the layout value in the .Media Preferences.plist inside the media folder. If that value is 1 everything is moved to a /Music folder inside the media folder. If 0 then the <Artist> folders go directly in the media folder. I would change the media folder to your current iTunes Media folder. Edit the .Media Preferences.plist file to change its value to 0. Then turn Keep organized off, apply, and turn back on. This will bring <Artist> folders up into iTunes Media.
Subsequently you could rename iTunes Media as Media, copy your .musiclibrary package from your system drive into iTunes, option start Music to access the library at <External>/iTunes/Music Library.musiclibrary, close, and rename iTunes as Music, which would fully transform the library to one that runs completely on the external drive and looks like it was created in Music. You may still have some old iTunes cruft to throw away which is covered in the user tip.
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