"It depends". If you've got a good shop and a handle on the sub-contractors of the deal (avionics, interior, paint, etc), that it can turn out ok. If you've got a guy flathatting running around for the lowest bids halfway around the country, then it's going to probably not turn out well. Avionics seems to be the worst.
There's a lot to be said for a de-bugged machine ready to fly, even with a slight cost premium. Someone has already had the headaches and spent the money on shop time to fix all the problems that invariably creep up.
Richman