True; and that would be the most likely outcome.
That said, it would be a shame not to take advantage of the interesting aspects of atmospheric flight - lift, compression, turbulence, etc. It would be
very easy to simply say that the FSD conduit forms around the vessel and excludes the atmosphere, but it seems a bit of a cheat, dunnit? It would be SO much more fun to glide down through the atmosphere and climb through it to the edge before charging Supercruise (and forbidding Witchspace until completely outside the atmosphere)....
OHHH the fun we could have with atmospheric flight!