That's an exaggeration of the difficulty of the terrain. The Canadian Shield is really only from east of Tweed to west of Perth, a distance of roughly 80 km. The rest of the route is largely farmland with lots of concession road crossings. For example, here's where the current trail crosses County Road 38 near Springbrook. Not exactly rugged or uninhabited.Between Peterborough and Smith Falls is mostly uninhabited Canadian shield with minimal road crossings, with the existing rail corridor being a terrible alignment for even medium speed passenger service. My bet is most of it needs to be new corridor for HFR or HSR - so they figure they may as well go all the way and build HSR for the stretch.
I mean we'll have to see, but my bet is the report penciled out a much higher cost for HFR than Via was claiming, meaning that HSR is a more marginal upgrade cost wise.