You're forgetting ram-air effect - the faster you go, the more effective pressure you encounter.
The jet engines on the SR71 don't work with an input pressure below about 0.75 Atm... but at the speeds it flies, the problem is overpressure, not under.
Maybe I am; let's see.
We're trying to scoop fuel. A dton of hydrogen is a metric ton of liquid hydrogen. Hydrogen at 0c and 1 atmosphere's 1/1284 the density of the liquid stuff, yes? Let's take that AHL fuel shuttle, needs to take in 350 dTons in - 140 minutes? That leaves it 20 minutes for the transfer, if I understand the canon elements right. So, 2.5 dTons per minute, 0.04167 dTons per second. Compensate for it being gas - 53.5 dTons of gas per second at 1 atm and 0C. 13.5 cubic meters per second, 722.25 cubic meters per second. Adjusting for thinner atmosphere, 144,450 cubic meters per second. So, a 1 meter square vent needs to be moving at 145 kps to do the job. A vent 2.4 meters square could do the job at 60 kps. I don't know the temperature up there, but colder temps would only make it easier. The scoop might not be 100% effective in collecting atmosphere, but there's plenty of room on a fuel shuttle for larger vents. Of course, you're not scooping hydrogen the whole 140 minutes, but then there's still plenty of room for the larger vents that would compensate for that. Since the fuel shuttle's pretty close to the highest proportion of fuel to volume of craft, it only gets easier for craft with a smaller proportion of fuel tank to craft volume.
All in all, assuming I haven't made a mistake or missed some detail, it looks like I was wrong: it's possible to skim fuel at an altitude high enough to maintain that key escape velocity. Just make sure your arc is shallow enough that it carries you back out to where you want to be. Takes about an hour and a half at 2G: in, then out. Twice that for 1G craft. 3G and up, likely to be a good deal faster since they can dive deeper and pull up without needing to worry as much about the local gravity.
All of which renders that half-atmosphere mention in Secret of the Ancients rather misleading, but it's not the first time some canon element misspoke.
That was kinda fun!
