I think it's more likely a "Hurontario style loop" going to Hunter, as being the spur.
And it is NOT a PanAm specific train.
The reason why Hamilton has two GO spurs:
West Harbour GO and Confederation GO
++ Already on the route to Niagara Falls, so extendable to Grimsby and St. Catharines eventually.
++ The only ones with room for parking garage, when Aldershot overflows (it already is close to overflowing by 10am)
++ Owned by CN, usually easier to negotiate with than CP
Downtown GO
++ Metrolinx owns the nice art deco train station, and the four sidingsit's very central
++ It's really close to the proposed LRT B-Line, that a simple Hurontario-style loop can connect directly to it, by running south (by turning into municipal bus terminal, and turning
++ It's connected to the GO bus terminal.
++ NO parking, but VERY pedestrian friendly station.
-- No feasible route to Niagara Falls
-- Owned by CP
So you can see, there are/were extremely good infrastructural reasons that both stations exist.
Besides, it isn't odd: Consider Toronto has 7 GO spurs, so Hamilton having 2 is really nothing! The allday GO plans is apparently not till the 2020s according to the recent announcement, a full whoopingly whopping ten years from now (When Toronto eventually may have 9 spurs -- the UPX spur, the Eglinton spur). In ten years, Hamilton population will likely be much bigger, justifying the LRT even more. Stop dictating things for Hamilton, silly guy. Let actual Hamiltonian voters decide. If we collectively don't want an LRT, then so be it. But let us decide.
Especially since they are going and it isn't till the 2020s that Hamilton gets all day service, and eventually counter-direction commuters. There's cities in other countries where the train lines spurs out at both endpoints where the endpoints are cities.
It may be odd to view it this way, but if you view it this way -- Hamilton is getting a fair and proportionate number of GO spurs compared to other areas within the GTHA that has multiple GO routes and LRT connectors. Yes, it did catch me by surprise when they decided Downtown GO was probably the all-day terminus, but it makes a lot of sense if the A-line isn't built right away, and starts with B-Line first. It is also theoretically possible to switch all-day roles depending on the outcome of negotiations with CP versus CN, as well as when the A-Line gets built.
About the Hurontario style loop, it solves several convenience-related problems -- it drops people directly in front of Hamilton GO, and makes it possible to run an LRT through the MacNab municipal bus terminal too, as that's one possible pro of LRT loop, to take advantage of bus connectors, if there's room after a bus terminal rejigging.
It's very hard to negotiate rail time with both CN and CP, so the role of each station can vary depending on rail capacity we manage to win from either CN or CP, how much timetable interference Metrolinx is willing to accept (delays in Hamilton will cascade down the rest of Lakeshore West, e.g. Burlington residents waiting longer) and at least one Metrolinx document admitted that the "roles" of the stations may change over time. Metrolinx has been thus far completely unable to practically add more trains to Hamilton downtown GO, until potentially billion-dolloar-league corridor improvements, and it is possible that James North (West Harbour) ended up the cheapest and most fiscally wise option. Have you not possibly considered that???