If I can recall correctly, didn't Kojima give the same spiel about MGS 3 being his "last game" in the series? So, he couldn't have possibly known (or even conceived) that Paramedic would be Dr. Clark. He doesn't think far ahead beyond the game that he's currently releasing for a time. It's this lack of foresight, that's the cause why the canon is such an incoherent mess.
Wasn't Clark mentioned as a "he" in MGS1?