I had always wondered about this myself too---- the same holds true for the German side and transferring to the OKH first, especially for corps and above. In earlier versions, it seemed that the Stavka/OKH would virtually always make their administrative checks and hence allow for a half price transfer of corps and such around, but in the current version of the game this no longer seems to be the case, and the higher headquarters seem to fail their check much more commonly then lower HQs, which somewhat limits this "exploit" (if an exploit it is). But there are still many cases, such as transferring single divisions, where it does still work, and seems to needlessly add extra mouse clicks and hassle where there shouldn't otherwise be.
A good fix, I think, would be to set the maximum AP cost of a transfer to however much it costs to transfer that division/corps/army to the higher HQ. Then one could be tempted to use the transfer via OKH/Stavka trick only when the lower level commander has a particularly low administrative rating. Otherwise, it just feels like nonsense.