Yes, they were originally intended to be duplicates of the main characters. However, during development the plot and design of D:OS evolved, the specific personalities of the main characters were dropped and the back stories changed, so there was no reason not to allow character customization (that was decided part way through the D:OS Kickstarter, actually), which resulted in them no longer being doppelgangers. For the EE, they were changed to match the new cover art.