I agree, if someone is buying a machine because they don't know how to build one they shouldn't have custom water. Its too complex a thing for someone who is too uncomfortable to build their own to maintain. CLC water-cooling at most (which will help in shipping).
If you insist on selling custom water-loops, leave it dry and include some mechanism to easily fill it up (Fill line using a T-Connector, or a conveniently placed reservoir port) and instructions on how to properly power cycle water through the loop and how to bleed air from it.
Remove the graphics card from the rig and send it in its own box. If you stick it in the machine and it is ever dropped, there is a good chance the PCI-E connector will snap. Same goes for any large air heatsinks on the CPU, except its the whole motherboard that will snap. This is one situation where a water-cooler would be a good option, as there is no weight on the motherboard.
I suggest building the rig, doing all your driver installs and quality control, then removing the graphics card. Include instructions on how to mount the graphics card with the rig, this way all the end user has to do is plug it in and hook it up to power, everything on the software end is done.
If the graphics card is under water, then I think you will have to make the user include that in the loop themselves. I'm thinking you have your tube going to a barb, which then connect to a Female-Female G1/4 adapter, which then goes to the rotary Male-Male G1/4 adapter. It will almost act as a quick disconnect.
This way its easy as screwing in half the rotary fitting to include it in the loop, rather than getting the user put tubing over barb, clamping and all that. Means they can get the GPU into the case and the loop within a few minutes, rather than 20min fighting with tubing.