"site specific" doesn't mean anything in this "domain"..
you'd think about you'd have users (samba).. /home is the place.. do you have mail too? well.. /home is good too
anyway.. I repeat.. as long as everything is clear (and must be since setup if not unattended one, IOW user must be steered properly) and documented, one place or other is the same..
the issue is when you have zillions of people that worked for years on the same distro (the underlying O.S.) and are in habit of using /home
finally: creating an "all web driven interface and idiot proof product" has the drawback that users won't ask themselves anything and will ignore what's going on behind the scenes (like windows did since epoch and still does).. this will simplify many things and it's destined to work flawlessy as long as you do the things following the designed path.. once you have troubles and have to debug or, simply, want to customize the product (it's OO.SS and everything is customizable) you can find yourself in trouble.. the monkey ready interface (and logic) must be a right balance between the desire to make things easier and the necessity to maintain some kind of control, knowledge and awareness of what's you're using
in another post Giacomo said that you hide a button to avoid your customers to open too many support tickets.. this is not the right approach and this kind of thing is quite a good example of what I meant above.