At a guess, it sounds like a good idea for small scale and slow production ... but if you run the numbers for a commercial scale production plant it will start to look bad.

I don't buy any numbers for commercial production since there based of leveraging the oil economy and will skyrocket over time. Maybe the first round of plants are feasible but what about the next round and after that ? The expense of digging a ditch can be as cheap as you want. And it can be spread of the lifetime of the ditch wich is at least decades. The only additional cost is plastic sheeting which can be itself produced from biomass so it will become fixed. In any case even when oil/natural gas becomes expensive for fuel its still a valid source for plastics for a long time esp once fuel pressure is removed.

Can you really fill a pond over 3 years and then immediately start draining it? Or do you need to fill them, and let them stew (producing methane of course) for some number of years? How many ponds does a 100 million gallon per year plant need? If it can't do 100 million gallons, is it even a silver bb?

Sure you can fill them at any rate you want it depends on the depth of the pond vs the biomass etc. That's a mechanical problem. The rate of breakdown or compaction is the issue. Take the natural setting your typical poorly maintained farm pond my experience has been that the layer of undigested organic matter is generally very low but the question is not what the fill rate is but what is the compaction rate ? I know semi dry composting takes about a year or less. A cows stomach or rumen digestion is a matter of days. A muck pond would be between these two extremes. Currently its rare to create the conditions for producing muck on purpose but in natural settings it seems to work quite well even in northern climates.

(in contrast, I'd expect the total cycle time for corn ethanol from grain delivery to shipment to be no more than a few weeks ... assuming they let the yeast work down to the last sugars)

Your thinking like and American whats the quick fix damned the costs. First everyone just about agrees the real answer is cellulose based solutions so forget about starch. My approach is a semi-managed local bio-reactor vs a monoculture solution. Considering the bacterial flora of a cow gut or termite and swamps I'd say mother nature thinks a bacterial witches brew is the best answer. Also on the chemical side you have syn-gas from the peat plus methane from the working ponds as feed stocks you can then produce whatever chemical is in demand plastics ethanol/butanol methanol FT what ever pathway. Also since you can combine the peat with methane your CO2 blow off is greatly reduced since you can boost syn gas production via C02 + CH4 -> 2C0 2H2 The methane is acting as a hydrogen source. You can do the same with coal and a natural gas source to control the C02. And that's the last point this approach works reasonable well with a tandem coal based economy till coal can be eliminated because again its really just a way to make low quality coal. And finally to address the economies of scale the peat or dried muck is already a microfine particulate so it goes right into a fluidized bed reactor or it can be moved and added as a slurry your paying the price for final drying but its like a wet coal. Potentially you could dry it and slurry with a low boiling organic solvent that's flashed off at the reactor or combine it with a natural oil like soybean oil. So it would be a carbon loaded natural oil. In the low boiling organic carrier case the carrier can be reused. In the case of a high boiling organic carries settling ponds would remove the bulk of the carrier for reuse. And to finish if you can pipeline the muck you can send it to a central plant but you can also process it locally. In any case using local muck ponds to massively increase the carbon content and break down the cellulose makes a lot more sense then exotic single species fermentation approaches for fuel.