I have never used anything other than charcoal in the media container, but you can put anything you want in there. I think you could even use bio media in there. The Eheim bio media would fit well in there I think. I used the polishing cartridge about twice and threw it away. It clogs so fast it's almost not worth fooling with IMO
. I couldn't see any difference in the appearance of the tank either. It might be useful for free floating algae though.
I don't know how much C02 you'll lose as the filter purges, but it won't hurt the filter at all. It's designed to purge when it gets air in the system. That's what the little acrylic tube that runs up the side of the center piece is for. As long as the C02 levels in the tank are acceptable to you, go for it.
You may find, after the filter gets some age on it, that the O ring doesn't want to reseal when you put the top back on. Lightly grease it with some Crisco and it will seal up fine. Since the Crisco is not water soluable, I don't see it hurting the tank or its inhabitants...at least I've never had any trouble.
My HOT Magnum has been running 24/7 for the last 4 years and I've never done anything but clean it (infrequently