There will be some power dissipation in the leads of the TEC. Some of the heat resulting from that power dissipation will be conducted into what is now the 'coldside' of the TEC. This will reduce the ability of the TEC to cool the CPU.
The degree to which this is a problem will depend on the gauge of wire connected to the TEC, and how short the connection is between the body of the TEC, and what should be thicker wire going to the power supply.
I'd recommend turning it around.
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