Yeah, not sure how you arrived at that conclusion seeing that Darth Starkiller was the original Galen Marek having replaced Vader, and the Dark Apprentice was a perfected clone. The endings are in no way related.
[Edit] In fact, here's a diagram for you:
The question mark is presumably TFU3
, assuming LucasArts decides to make it. They tend to have a habit of leaving things hanging though, and so far that's how this franchise is looking, unfortunately. We've been told about no plans for a third installment so far.