Its worth remembering that the end of atmosphere isn't a hard line, it just gradualy gets thinner. Also the hardest part of getting into orbit (from a planetary perspective) is getting enough horazontal speed to reach orbital volicities. Because of this, it's not unreasonable that an Imperial ship can come down low enough for high-alititude adjusted aircraft to launch. But it's not going to be hanging out there, because once you have enough atmosphere for an aircraft to operate in, the ship is going to be experiance drag and, quickly, be on a sub-orbital trajactory. Besides simply passing over the drop point, the voidship is also soon going to have to ignight it's plasma drive to gain enough speed to put itself back into (at the very least) low orbit.
Its perfectly possible, however, that particular versions of valkalries and other Imperial aircraft can temporaraly lift themselves to the virtical height of low orbit. Indeed this might be as simple as intigrating something akin to a JATO rocket that is fired after puting the aircraft into a virtical stall. It would just have to be well timed, so the transport voidship is there to "swallow it" as it reaches the apagee. Otherwise, the voidship might do another upper-atmosphere dive & return.
On the subject of Space Marines and their Drop Pods - Imperial Armor books note that, while the pods are often considered disposable, they can be recovered by Transport Thunderhawk in pairs. This is the same vehicle that is used to land and lift Space Marine Tanks. Space Marines themselves go by standard Thunderhawk (usualy). All of these vehicles specificly have Ceremite plating to resist 'hot' reentry.
That is basically how the Lightning and Thunderbolt are recovered if launched from orbiting carriers: they include a dedicated rocket booster for launch assist and transatmospheric insertion. The Marauder has engines designed to transition between air-breathing turbojet/ramjet and closed-cycle rocket modes. With the Valkyrie, I suspect it would require pre-launch modification to fit suitable boosters (which would cut down on their payload) to lift it for recovery, so they might be limited to landing at hastily prepared FOBs groundside.
Interestingly, prior to the adoption of the Fury and the Starhawk, the Thunderbolt and Marauder were used as void-combatants (the Gothic Sector Fleet completing the transition just before the outbreak of the Gothic War, while some carriers assigned to the Cadian fleet were/are/will be* still running void bomber ops with Marauders during the 13th Black Crusade). With the Marauder I can see that, but the sheer lack of size of a Thunderbolt must make it fairly sub-par, as I can't see them being able to fit much of a delta-vee budget into that airframe.
*depending on when your current campaign is set.