You could make the argument the point of the rule is to penalize (i.e., balance) the ability for the troops to disembark nearly anywhere on the board with reliability. To my knowledge, no other flying transport has the ability to drop your troops exactly where you want them without sacrificing the need to skyfire at it -- so to balance that, if the flier goes down the troops inside start in reserves.
Now, that is definitely over thinking it - most likely GW had a fluffy reason for it... but we could spend hours upon hours coming up with fluffy reasons for or against it so that is not really worth our time.
Think of it this way -> Scythes cannot land to disembark troops, as such it has the technology to beam them down. The shorter distance makes this much more reliable than conventional teleportation (e.g., terminators from space) so there are never conventional deep strike issues such as scatter. However, Scythes cannot beam their contents down precisely as they are crashing, so the occupants usually do not end-up at the crash site. Some are destroyed before they can make it to the teleporters, some are teleported in 100 different directions and destroyed, and others go into ongoing reserves (just like deep-strike mishaps) and enter from a table edge.