Do the character interactions have any effect on the game?

While playing the bureau you can interact with characters in different ways. For example there is the side quest where you can talk to the comms officer about the radio transmission. During this interaction you seem to make a choice, or at least suggest a choice to the comms officer. (About how she deals with the survivors).

Later the same sort of interaction occurs with DaSilva, you can tell him to sacrifice himself, or tell him that you will try to find a cure for his infection. I chose the latter. So he turned up in my base as one of the infected.

Now I was wondering, do these conversation options always have the same effect? Do the options have cosmetic effects? As in, there are different people in the base between missions. Does it influence the ending? Or is it just fleshing out of the world?

I know some of them unlock side missions, and others unlock new items. But those have a clear effect so I'm not wondering about those.