The actual directory names don't really matter that much - AmigaOS references them all by assigns - DEVS:, C:, LIBS: etc. I haven't tried renaming and manually setting the assigns to the new locations, but in theory that should work!
I'm not so convinced of that. Yes you can add paths to the assigns, and even remove and reassign them else where, but if the standard dirs aren't there, you might have trouble booting in the first place, to run the script that does that.
The absense of SYS:S and SYS:C in particular may cause a headache.
