I may be misunderstanding you question with the inline instead of by-pass (I'm sorry! I'm still learning!) but we make our system a bypass so that if the filter clogs, everything will still function as normal and your coolant will still flow. I would wait before trying anything like that until you call and talk to Bob or John to see if it's possible or recommended.
We design our housing with two of each port so that it can be customized with other applications and configurations. Some people choose to mount in different locations than our instructions and the two port options allow this for them. I think you can stick temperature gauges in there too...