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.
If SYS:C is missing would AmigaOS look Startup-Sequence from the root?
