They answered that one long ago on Champions. There are 3 types of points: CO points, STO points, and c-store points. You can use stipened or future reward points in either game only for that game, but C-store points can be used in either.
Too answer the other question ppl may have, when you spend points and you have both types, it pulls from the game-specific points first.
People keep telling me this but this answer was specifically given regarding stipend points in CO back when STO would NOT be f2p. Times and things have changed a great deal since then which means this question needs to be answered again as that previous answer has most likely changed.