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I don't think we are to believe that the crew of the North Wind was stranded in the arctic for 2 decades to rescue Alex at the end. I think you are correct about Kronos but a little off about "the comfortable ship". The ship was always The North Wind, but for whatever reason there was the possibility that The North Wind wasn't going to exist to pick up Alex. A cyclical paradox: The North Wind can only exist to pick up Alex if Alex can somehow influence the events of the past to save the North Wind. In the end they save each other resolving Kronos' dilemma: consolidating the two timelines into one and resolving the paradox.

Edit: I think I may have been too focused on the Why and How of the paradox. I think in most western entertainment/cinema we expect everything to be explained at the end, but this particular story isn't really reliant on the Why or How. I think we are simply to understand that Something occured that resulted in two diverging timelines of which Alex (the player) is the only one capable of repairing. We don't need to know the specifics, only that 1) Alex was to meet the North Wind for pickup in 1980-something 2) The North Wind became icebound in 1960-something. Why or how this happened isn't important to the player, they are simply acting as an agent of Kronos to fix the paradox.