What I'm about to reveal is part of GSL's ending, so you better not flame me for this, cause you asked for it in a way...
[HIDE]At the end of GSL, the future Tendou disappears, because by taking the second meteor from his time to 1999 before the first meteor hit, and crashing the two into one another that creates the Shibuya meteor that causes the events of the TV show, Tendou has changed history, meaning everything that happened in the movie's timeline never happened in the TV show's timeline. Thus, anything that happened to the characters in the movie never happened in the TV show. [/HIDE]
That should explain that Dark Kabuto is NOT the Souji from GSL.
Now as for the reason for Dark Kabuto bearing the name Souji Kusakabe, do keep in mind that this Souji is...
[HIDE]A worm impersonating Tendou, right down to his memories[/HIDE]
...which means that he only lives to protect Hiyori, his real little sister. And as for Souji Tendou, of course, his name is actually Souji Kusakabe as well, but he was adopted by the Tendou household, giving him the adopted last name "Tendou"