I think that the in-town train station idea has been shelved – NNEPRA's main rationalization for building a new station is avoiding a time-consuming turnaround at the existing location, and moving the station to West Commercial Street would just re-create the same problem.
A West Commercial Street location would serve Portland-bound tourists, but I don't think that's the most important market for the Downeaster to go after – they're looking to build ridership by adding more "commuter" trains between Biddeford, Portland, and Brunswick, and an infill park-and-ride stop in West Falmouth. Putting a station on St. John Street would put the train within walking distance of the state's biggest employer (Maine Med) and better cross-town connections with METRO.