1) To prevent gamey tactics of "AP crunch", when destroyed units didn't return at all, and you were forced to pay again to build them from scratch, which sometimes meant it wasn't "real" resources (like men or armament points) the actual chokepoint on rebuilding Red Army but some missing paperwork (prevents snowballing effect of losing many units).
2) To discourage gamey tactics of hoarding tons of APs until the right moment (for example Rifle Corps price going down from 20 AP to 10 AP), because APs represent (amongst few other things) effort over time, not some commodity that can be stored and used at any given moment in huge quantities. You can still store them, but there is a risk.
It is simply assumed STAVKA is expending some effort to recreate destroyed units, but on the other hand in case of emergency it can do this more efficiently.
Because of 2) there was no way destroyed units could give you back their cost in AP, to be used in rebuilding units, because then you could re-route those APs for some different activity (like HQ Build Ups). We have removed most ways of gaining APs (except every turn, and when fronts arrive), like when toying with static unit mode, because APs should be only used up, spent to perform various activities that your general staff is doing during the week. So that's why we went with this "soft" loss method.
Sounds reasonable :)
Now that you're here, Morvael... I've heard rumors that the German supply model would get some tuning in the next patch, any hints what kind of changes we should be expecting?