Running your chiller in-line would be ideal as long as the flow is within the recommended range for the chiller because you won't have to run an extra set of hoses and have an extra powerhead in the tank. I think the reason that you wouldn't run a chiller under the recommended flow is because if the flow isn't strong enough, the returning cold water will lose it's coldness before it gets back to the tank and if it's too strong then the water isnt in contact with the chiller plates long enough to exchange the heat.