but an off-the-rack recumbent was significantly more comfortable than a carefully adjusted DF.
That's my general experience, given a seat that's vaguely the right shape. The niggles start to show up with prolonged riding, rather than the ten minutes (or, given a sufficiently bad saddle, ten seconds) it takes on an upright.
My leg length imbalance is the tricky one for me - with a recumbent seat you can't compensate by tilting your pelvis like you would on a saddle, so it shows up in the knees or ankles as not-being-able-to-get-the-boom-extension-quite-right. (I seem to be having some success with different length cranks.)
There's a classic numb bum thing that some people get from some recumbent seats at certain angles. I've not experienced it myself, but my preference is for relatively reclined positions, with the weight being taken on my back, which probably helps. Some people find padded shorts helpful (though not all pads are suitable for prolonged recumbent riding).
Aggressively reclined seats mean you're craning your neck to see, in exactly the opposite way to riding in an aerodynamic crouch on an upright. You're likely to get a lower drag coefficient for your discomfort, of course.
Barakta's quite sensitive to having enough shoulder support from the seat, presumably because of her weird anatomy. She prefers mesh over hardshell, which means that you've got to check the seat tension occasionally. I find her seat lacking in lumber support (much like the average car seat), but it's still more comfortable than any saddle for a day of riding.
I think I've mentioned handlebars upthread. My wrists get tired after hours of riding the Baron, because the optimal angle on the tiller would foul my thighs when cornering, but USS is generally fine as long as I can reach.
I think BB height (relative to the seat) on a recumbent is a bit like handlebar height on an upright, with the right answer depending on the kind of riding you're doing.