Just in case you did not know this part. They are "bound" in a sense. If you get a stipend in the game, those points can only be used in STO. They will not cross over to, say, Champions, like points that you purchase will.
As was said previously, the stipend points are bound to STO, as are the dilithium exchange Cryptic points. Both of those give "promotional" points, which are bound to the game in which they are earned (I'd imagine the same is true for Champions stipend points.)
If you pay actual money for regular (non-"promotional") C-store points, you can use them in any C-store on the same account. I used some of the last batch I bought for this game in the Champions C-store.