Custom cooling adds $400 to the price for the lowest level of cooling which is CPU only. That's insane. Granted labor adds a bit but seriously the parts aren't that bad you might hit $300 or so doing CPU only going with top end parts. So it's at least a $100 premium and you have no idea the components they will use to build said loop. I try to stay away from the mystery box.
I would not be so sure about that. I spent over $100 on my Bitspower fittings along on my last custom loop. Throw in another $60 for the block, $80 for the radiator, $50 for the res, $80 for the pump and $30 for plastic tubing. Oh yeah, and add another $18 to $35 for coolant. If you want hard tubing, that costs more, with WAY more labor. PrimoChill tubing is easy to work with, but the hard tubing is quite difficult, not to mention the fittings cost more. Oh yeah, and you need fans. Good sleeved fans will be at least $20 each, if not more (I like Scythe Gentle Typhoons).
The only way you could do $300 for a new CPU loop is if you bought one of those EK kits. They have great water blocks, but the fittings and fans leave much to be desired.