The primary purpose of trapping the air at the closed end of the radiator is to prevent the air from getting to the pump/block of an AIO. Fluid permeation will still take place through the hoses, and only the hoses, not through any other parts of the cooler. The reason you do not want the the air to get to the pump is because it will cause unwanted noise, and it can also cause accelerated wear.
For custom/open loops, you want the exact opposite radiator placement to ensure the air get out of the radiator, and into the reservoir. It is also why the order of the loop matters, not because of performance difference, but to help bleed the system quickly without extra noise (pump should 'suck' from reservoir to prevent air from getting into the pump, which would usually require it to be pulsed to get the air out, creating unnecessary noise).