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.
Some people have made boot disks etc with reassigned system assigns, and I haven't heard any complaints of them. So I'd guess it should work that you first remove S: assign, and then assign it elsewhere. Although I don't remember trying it myself, but nobody (at least programmers) should never use fixed paths in these situations... probably at least most of the stuff would work happily.
Maybe only the startup-sequence has to be where kickstart looks it at first place, but then you can reassign other dirs first thing in it...
