As for the loss of flow from running through a chiller I have heard to add about 4' of head pressure as a ballpark. Searching further on the site you linked it seems that the recommended flow rate for the chiller is approx. 360-480 gph (6-8 gpm). http://fritzpet.com/chillerchoose.html. That is a little lower than I was thinking. I have a Current USA Prime Inline that basically is allows for 480-840 gph. I also noticed that the chiller is recommended for systems from 200-300 liters (50-75 gallons), and from your signature I am guessing that you are setting up a 120G so you might want to consider whether the chiller will handle the water volume you will have.

As far as pumps go and going directly back to the tank from the chiller: I do not know what you tank return setup is, but I run one return pump that goes directly to the returns on the far side and a second return pump that goes to the chiller and then to the near side returns. You are right that the MAg 18 would inhibit chiller performance.

I am not that concerned about getting pods up to my display from the refugium (focused on nitrate export) so I have the water pass through the bubble sponge after the fuge and hope that it gets enough out to be acceptable to the chiller. You will still probably want to follow your chillers instructions on cleaing/flush procedures about twice a year anyway.