Does this sound correct, in clean water and high oxygen. You just said bacteria doesn't form on the bottom and the pump is on the bottom with the least amount of oxygen feeding your filtration. How do the bugs form in a low oxygen, dirty environment of a filter. Regardless of size of mechanical filter, debris is still getting into the biological side of the filter which in your words means no bacteria lives because it's dirty and lacks oxygen.
The nitrogen cycle happens every where, not in 1 area. I leave all the debris on the bottom of my pond from fall, where does it go? Not in to the 5g filtration.
So in the pond, your filter area is the only spot bugs grow, how big is your filter? It's less than 10% of total volume which in any hobby is low. 10-20% of total volume will not digest that amount of waste period, thus the nitrogen cycle happens throughout the pond.