Yeah, not sure what your issue is with covered moats. You could use the Yor9k St covered moat to connect to the West (Citibank) and Northwest PATH links, the northwest link currently just takes you to street level across the intersection but is going to be extended to meet up with the main network in the next few years.
As for the main network, the only means of access, as you said, is either via the TTC station or street access. Again, I'm not sure what the issue is with covered moats or the TTC station...indeed, they would have to tunnel under the streetcar platform, subway platform, and TTC concourse in order to get directly between Union and the main PATH, I don't think that's realistically possible. You walk out into the covered moat, around the outside perimeter of the TTC station, and you're in the PATH.
There is however direct indoor acc.ess to the skywalk, including the Delta Hotel and Convention centre indoors. Also the southern PATH--you can exit from the south end of the VIA Concourse Hall, the "Union Plaza" exit, and there is a set of doors that leads upstairs into the PATH walkway through the ACC, which has indoor bridges connecting to Maple Leaf Square (with future path connections through Longos into ICE condos and Infinity condos ending at Simcoe south of Bremner), and through One York St down to RBC Waterpark Place. There will be bridges to the new southeast waterfront PATH network, but it remains to be seen if the entire connection will be indoors, or if Platform 3 will remain a covered through open-to-air connection.