I also went to the Alto consultation and just about expired from happiness when the rail design engineer in an Alto lanyard, unprompted, raised the possibility of an elevated approach to Union Station from along the lakeshore (among many, many, many other possibilities for Toronto stations and approaches). Probably won't happen, but I personally would love to see it, and I'm still a little sore from how badly this suggestion went over on the Union Station Revitalization thread a while ago.
Anyway, it was nice to hear that the Alto people seem interested in building something that facilitates extensions to Windsor or Niagara. Tunnelling under Union would not fit that bill for a lot of reasons, including the need to go deep under the TTC.
I also heard loud and clear that CP is uncooperative for anything to do with passengers in the city. Options like terminating at the Summerhill LCBO, or terminating at the Don Valley station on the Ontario Line, are theoretical possibilities but would require CP cooperation, which (apparently) nobody expects to get. (Also, not to be a downer, but the Ontario Line neither exists nor works yet).
CN is apparently more open to negotiation, but their lines are less convenient for downtown access. You would need to build a station in the north part of the GTA and find out a way to get into Union Station to drop off and pick up passengers. This concept allows people to drive in from car-dependent areas and make use of the service, without having to get to Union Station for every voyage.
Seems like there might be an interest in using something like Langstaff station as a primary station (containing support services and parking), with Union as a secondary station (just short stops with no added services), because of the connection to GO and eventually the TTC subway and, I suppose, the future Ontario Northlander. If not Langstaff, then something similar.
Another visitor, a civil engineer, mounted a passionate argument for why the federal government should finally stand up to the big railways for the Alto project. If there was ever a time to put the public interest first, it would be now, considering that local governments failed to protect any other corridors for railway expansion in and out of downtown Toronto. The rail design engineer, however, essentially said that the railways have ultimate power and not to expect Parliamentary intervention. As an example, the engineer spoke of past work on Kitchener expansion, and how much accommodation CN got for spurs, even though Metrolinx owned the line.
The engineer also had something else to say about the small-town side of things, which frankly I hadn't considered and think they should mention more often. Building the line will be a major undertaking with lots of jobs, etc. Maintaining the line on a daily basis will be an even greater, and perpetual, undertaking. All that maintenance will likely be done on contract with small, local businesses. So each small town might not get a stop, but will get a lot of new and constant business keeping the line working properly, and (hopefully) will get some kind of public transit to the nearest Alto station.