Okay, lets break it down some...the diastatic power of flaked rye is really negligible, and mainly is for flavor. With the low diastatic power, enzyme activity is barely present, and does not lead to very much sugar production. Not saying that if you use enough you wont get sugar production, just that you would need to use a large amount. But with the modifed rye malt, it has a diastatic power of over 100 and allows for a good starch production, which allows for a higher conversion to sugar. So, because of this, you get a higher concentration of sugar production from malted than from flaked.
The flaked is always sold basically as an adjunct, and leads to flavor. The great part is that it breaks down very easily and boosts flavor so nicely. In my opinion, as well as past experiences, I always use it together with malted rye for a more complete rye flavor.