I'm trying to use the radial atmospheric scoop from orbit. I built a prototype using 2.5m parts. When I check the window for Atmosphere Extraction, the intake is ~30mT/hr.

Okay, so at that rate I can fuel my starship by the next ice age. That's okay, I'll just scale up to 40m parts:

But intake atmosphere consumption is still ~30mT/hr. Is this an oversight on my part or are the tweakscale configs for this part configured incorrectly?

It is indeed an oversight. It will be fixed next release. If you can't wait, simply add
TWEAKSCALEEXPONENTS { name = AtmosphericExtractor surfaceArea = 2 }

to ThweakscaleConfigs.cfg

btw, If you want to collect from the atmosphere in serious amount, either use the Atmospheric Particle Scoop or Bussard Magnetic Scoop for collecting hydrogen and helium, also great for space station Ionosphere breaking

Awesome! Will try that next opportunity I get!

Update: tried this last night and atmospheric consumption appears to respond correctly to scaling. Think you can close this at your discretion.

Will try the other scoops but it looks like I'm getting satisfactory results with the radial scoop. Should be able to get half a million tons of deuterium within a few years. Seems a little OP for an orbital refinery, but if that's what the science says then I'm not complaning. :D