Parker - I'm no expert but based on my reading and studies of the subject (planning to build one myself), my understanding is that the water clarity all comes down to the nutrient balance that you can maintain in the pool with the plant life in the regeneration zone. In simple terms, you want to be on the verge of starving the plants of nutrients so there is nothing left over to support algae growth in the swim zone. Fish and animal activity increase the nutrient load on the system and although the plants will thrive - they may introduce more nutrient than the plants can remove and therefore leave excess in the water to feed biology (ie - algae/bacteria) that you don't want.
The reason for nature "separation" is to manage the above principle in an intentional way. The bog you refer to doesn't sound like it would work well as a regen zone due to the excessive nutrient load that it would introduce to your swim area. If you don't want to lose that feature of your property though, maybe you can isolate and separate part of it with a liner and use it for regeneration.
Hope this helps!
Cheers,
Anthony
