Fine, but it's retconning within the season. With that tech, there'd be no reason for them to look the way they do, which is a good orbit/lunar vessel ill-suited to atmosphere - a great design for their designed purpose pre-breakaway which can't fulfil its ongoing series role without magic tech. Frustrating thing is that it wouldn't be so magic if, for instance, we'd been told that Bergman's experimental forcefield from Black Sun would now be fitted to the Eagles, expanding their capabilities. As it is, we can I suppose fill in the gaps.
Maybe it would've been better if they'd used Eagles for vacuum operations and a different, more aerodynamic craft for atmospheric operations. They could've justified the latter as ships used for trips from the Moon to Earth.
As in: 2OO1:A Space Odyssey, they had the Pan Am Orion III shuttles[Earth to space station], the Pan Am Aries 1-Bs[space station to Clavius Moonbase] and the Moonbuses[lunar surface flights]. Gerry Anderson's UFO(1970-1973), they had SHADO Lunar Modules[Earth to SHADO Moonbase] and Moonhoppers[lunar surface flights]. Gerry Anderson could have avoided this structural problem if the Eagle had been designed more aerodynamic as his SHADO Lunar Module or Orion III. However in other science-fiction aerodynamic craft for atmospheric operations do not apply in: ALIEN(1979) the Nostromo landed on the planet Star Wars the Millennium Falcon I think the Eagle Transporter fits in their category.
Or maybe an Atmospheric Landing Module as another option for the Eagle mid-section? That lands and takes off, Eagle stays in orbit as a mother ship. But like shuttles rather than transporters, it adds a plot slowing complication.
Well, there is the Re-entry Glider that was mounted on top of an Eagle in the episode "The Immunity Syndrome."
In terms of 2001--the space station would seem to be a better fit for the Moonrakers--and the Orion III shuttle from 2001 seems to work better with Drax's more complex looking space station in the Bond film.