That's interesting if the board is part of the thermal design. If the heat is intended to reach the mounting holes, then brass stand-offs should help to pull that heat away. Another option is to use longer stand-offs and make the 'hat' connection via a short ribbon cable. That'll create a bit more space around the CPU. Yes, it would have been good to have the CPU on the underside (for my installation certainly), but I suspect they were conscious that this could affect compatibility with a lot of earlier installations/cases/fans etc.
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