Vertigo, I've been doing quite a bit of reading on that site as well.
I think FAQ part 3 answers quite a few of your questions
Here's an excerpt that explains why he recommends using a seperate pond filter.
Q: Would it be possible to create this anoxic system right in the main pond itself? Why the separate chamber? If a pond had a good turnover rate and pots of lilies all over planted in the material, wouldn't the same effect be gained? I’m thinking back to a few years ago when I actually did have kitty litter and lilies in my main pond and my pond seemed healthier? Could I have had an Anoxic system back then and inadvertently removed it?
A: Yes and no, yes, if you made an island and the filtration system was in middle of the island. No, because you would turn you whole pond into a big filter. This filtration system will grow and contain cyanobacteria in it, but the main bulk water should stay free and clear of such. The way I look at it; it’s better to have cyanobacteria in the filter than in ones pond, wouldn’t you agree? Soon as the filtration system starts running at full capacity, the cyanobacteria will subside like magic. In another words, the filter will starve the cyanobacteria out of available foodstuffs. Cyanobacteria is very pragmatic for many hobbyists and this filtration system helps control such but does not eliminate it
completely as explained on page-50 of my CD-book. That is why the waterfalls in the pictures, in the CD-book stay and look cleaner than convention filtration system. Containment is the key word here; do not let available foodstuffs (like phosphates) back into bulk water as other systems do and do not let nutrient-rich waters (Ammonia-Nitrogen) back into solution ether.
Here's what he has to say about the need for pre-filtration using this system:
A: I’m very pragmatic about really good too excellent pre-filter before any filtration system. It is paramount in keeping any filtration system clean and healthy. I cannot emphasize this one thing to the hobbyists any stronger if I tried. A good pre-filter will cut down on considerable amounts of fish waste, food, algae, and plant matter. It has been proven in saltwater system that cleaning the pre-filter before filtration takes place will keep redox at its highest point with very little outlay. It is no different in our ponds; it has been scientifically proven that; filters stay cleaner and healthier with good prefiltration. The key word here is: healthier. What makes it through the pre-filter, which is organic matter, now, will settle and mineralization will take place by the microbial flora. As you know this then becomes ammonia and/or ammonium and must be taken care of by the filtration system. Think of this; the ammonia ion (DOC) is being made in the filtration system were the biocenosis clarification baskets can immediately take care of it as positive ions, plus any negative ions that cross the electrical gradient by diffusion. The thing you must remember about this system in opposition to other systems. The baskets themselves are a constituent of the filtration system inner workings, but not the filtration system itself. However, as it (detritus) keeps breaking down it them becomes mulm.
There are other answers to your queries about water flow and basket depth as well, but I'm sure you'll read the the FAQ if you haven't already.
Personally, I'm convinced enough to give this system a shot. I've ordered some laterite and extra baskets, and I'm going to turn my top pool into (rather large) anoxic filter. I only have a very small amount of biological filtration going on right now, so it's not much of an adjustment for me.