Sorry to revive an old thread, but as a new kid on the block I was also wondering about this. As far as I can tell, the SkyDemon calculated endurance does not consider unusable fuel, which can be as much as 15 minutes flying time. For example in a PA28 there's 2 US gal unusable, which can be more than 15 minutes at cruise, depending on the model. In a 152 it's around 1.5 US gal unusable, or 14 minutes at cruise.
"Unusable fuel" is not the same as "fuel that can't easily be drained from the tank". According to FAR 23:
"The unusable fuel supply for each tank must be established as not less than the quanitty at which the first evidence of malfunctioning occurs under the most adverse fuel feed condition occuring under each intended operation and flight maneuver involving that tank."
In one weighing schedule I looked at, it explicitly stated that empty weight includes no fuel - not even unusable fuel.
On SkyDemon, if you include total fuel in the aircraft data then the endurance will be slightly optimistic. If you put in only usable fuel then the endurance should be more accurate, but the aircraft weight will be out by a few pounds (maybe 15-20lb).
Not a big deal (and no one has any business getting within 15 minutes of fuel exhaustion), but assuming one uses actual fuel loading, perhaps worth noting that the estimated endurance will be optimistic by a quarter of an hour or so.
Unless, of course, I've totally misunderstood what's happening - which is quite possible!