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I think even if the side jobs were left in, there is not real way to conclude them with any plausibility.
In both jobs one outcome is that the fossils and or the boys nail Sophie. Another outcome is something short of the first possibility. Now how the game its designed that the stories are not entirely linked with one another, still there is some interconnections. And if Sam got Sophia so worked up in his bedroom or Dyaln after date night and Sophie wouldn't give herself fully to either, how with the character build of Sophie would she allow either the fossils or boys get far with her?
In both situations of the side jobs and the other routes, the developer painted themselves into a corner. The problem of trying to set up every route to get to the point where Sophie crosses the line then toward the finish Sophie crosses those lines, is the collapse of the storyline and plots. It's the same recipe as the final season of "Games of Thrones."
By now, Sam and Sophia ought to be full lovers and Sophie should be having difficulties with her moral compass and her sexual behaviors with the other love interests while having the complications of Sam being in the background making Sophie situation harder on her.