It doesn't seem to be Krauser?
In Darkside, just as you said, there was only a voice over the intercom, and the guy speaking was definately Krauser, or at the very least, Jim Ward, who is of course the man who plays Krauser.
And I assume this is also why they changed it from the man drinking coffee in the interrogation room(who obviously resembles Jack), to the camcorder behind the one-way mirror while Jack speaks to him via intercom.
While they met in person in Operation Javier, Capcom seems to have altered the orignal interogation room scene to set it up that way in Operation Javier.
Also,you mention that Jack had a lower position than Leon, this is true by Operation Javier, where he is getting sercret orders from the President, but before Leon worked for the government, or rather when he was in the interogation room, Jack had the authority to do what they wanted with him and that little girl. In fact I think he says just that.