And what do you mean by it defeats the purpose for running it through my main tank?
The purpose of a QT tank is, so you can monitor the health of new additions (and medicate them as needed), without running the chance of contaminating your main display tank with whatever "bugs" may be hitchhiking along with the new arrivals.
If you use a HOB style filter (or anything else directly connected to the display tank) you risk the health of the main tank, Hence using a totally separate tank for quarantine.