Sort of-- the API data is sent through APIS to CBP whereas the SecureFlight data is sent to the TSA (to the TSC, I believe). The airlines might co-mingle the data in their internal systems but, as far as our government is concerned, they are two completely separate things.
I was indeed talking about the data items themselves, not their destinations, which are indeed different. Moreover, because of the timing of the entry of the data, I think it may actually be duplicated at the implementation level.