The con is that it will take more space.
The pros are that it will strangely enough cool a little bit better, simply because of the extended length i.e. more surface area for cooling (not noticeably though)
The extra lenght shouldn't be a concern, even if the extended rig is not sitting at the same level. The only thing you have to watch out for (just like anyone else) is to avoid having elbows in your water route, which is easier to avoid in a sepearte box.
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