There are some few similarities between aio and custom loops, just as there are similarities between air and aio, but that's where that whole line of thought comes to a sudden stop. There's a ton of stuff where custom loops are totally dissimilar to either.
Price is the first one usually seen. A good loop including cpu/gpu will usually average around $700 or more, depending on how its plumbed. More care, research, decisions go into a loop than the entire rest of the pc combined. Ppl can throw together a relatively decent pc in a few minutes on pcpartpicker.com, a custom loop can easily take months of research and planning. Custom rads are not created equal, are not finned the same, are not the same depth or flow restrictive, what fans are appropriate for that particular rad etc. The last thing you want to do is throw a couple of high cfm, low speed, low sp, rgb case fans on a 60mm thick radiator.
Custom loops are an advanced science, even if some show people treat them as works of art and performance taking a back seat.