I vent my radiator into the case (it's front mounted) and my motherboard temps are a little less than before H20. I assume this is de to a warm airflow everywhere from the radiator rather than a heat sink blowing it on the motherboard chipset and graphics card (before it mixes with other air, and leaves).
If you are really concerned, mount the radiator in the back or top to vent out, or in the front with a little ducting to side vent.
Many of us only have mid size cases. You just have to plan a little more, but shouldn't pose a problem.
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