If the fittings are on the bottom it will take more effort to get the air out of the rad, and later bubbles may re-accumulate. Due to the fact that flow in a heater core can travel in different paths at different rates it's easy to get an air lock if one of the fittings isn't up (to let air rise out).
Could you mount it sideways??? I'd either try sideways (both fittings to left ar right), up (both fittings at top) or flat on the top or bottom. This is also the way heater cores are mounted in cars, never with both fittings at the bottom (I assume for the same reason).
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Danner Mag Drive 350
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