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For any closed loop cooler mounted to the rear exhaust, you can probably expect it to block off being able to have a side mounted fan on the case lid. This is especially true for any case using the 240mm fans. The Noctua air cooler also has a tendency to block off the installation of these fans as well.
I think the best situation would be a case where you can install the closed loop on the roof or even in the drive bay as opposed to the rear exhaust. Choose a case carefully that will include some sort of side panel fan configuration. These fans on the case lids are almost always raised up somewhat to include the top GPU and the area around the CPU socket. That might be the best all around config to help cool every component.
I think the best situation would be a case where you can install the closed loop on the roof or even in the drive bay as opposed to the rear exhaust. Choose a case carefully that will include some sort of side panel fan configuration. These fans on the case lids are almost always raised up somewhat to include the top GPU and the area around the CPU socket. That might be the best all around config to help cool every component.