I can't speak from direct experience related to the Bombadil, but maybe this helps.
From what I understand, the bike actually preceded the tires - though not by a long timeframe. Kirk Pacenti designed the neo moto, and then the quasi moto, directly in
response to the Bombadil and some persuasive conversations he'd had with Grant. So if you have a REALLY early model, I could understand how the clearance be minimal. Since it was originally conceived as a bike "in the spirit of a 1985 mountain bike," and since mountain bike tires were only 1.75" wide back then, it probably made sense. I know that later frames have increased in terms of their available clearance. There are other images circulating of what is described as a test model, fitted with neo motos (which you've probably seen), and it does seem to have more clearance than yours - though its hard to tell for sure. Perhaps this was a first revision - before they did the batch of clearcoat frames?
The other theory I had doesn't seem to apply to your frame: Just like your bike, the seat-stay bridge is also the point of least clearance on my All-Rounder. But on mine, the builder used one that was drilled for caliper brake mounting, even though the bike uses canti brakes. In my case, I've assumed that it was (consciously or unconsciously) located where needed to provide the option of switching the brake-types, based on longest-reach brakes available at the time. But, unless I'm seeing it wrong, yours doesn't look like it is meant for that.
Even though it's tight, I personally would have no issues using it with the clearance you're showing. I'd just avoid gumbo mud, which I try to do anyway. If you're interested, I can post a picture of the modification I recently made to my fender, to allow it to clear the stay and still let me run an oversize tire.