They didn't specifically make it possible, bugs are errors or inconsistencies that appear due to imperfect code inside of the game.
Meaning not all possible outcomes or abuse was thought of during the game's development and it's features.
If the way-point system was meant to be used in such a manner that allowed players to way-point a unit into a transport and then specify a target on the unit's departure from the transport, then the way-point system would simply allow you to select the unit, order it to go into the transport and then click on a target, to attack, capture or infiltrate, but that's not possible.
Instead the way-point path is terminated after giving the order to board a transport and no future orders are allowed, unless you find a glitch to abuse to allow you to give the way-pointed unit additional orders. Which is what you are doing.
makes perfect sense to me