You really need to read the report on it, where you will see that the cost is very similar. BOTH options involve excavation and both are (I am sure) going to see cost increases. Steve Munro has a good synopsis at https://stevemunro.ca/2019/03/05/waterfront-transit-reset-the-union-station-connection/
In the TTC's presentation there is a "Rail Viaduct Risk" for the streetcar. Looking at the drawing there are 2 rows of piles that have to be moved for the streetcar which are not needed to be moved for the APV. No idea how this does not cost any more money.
Heck, for the Union Station Reno they didn't even replace any columns...they just extended them downwards. And we know how that's going.
To replaced the columns they will have to (1) make sure the 2 columns on either side can handle the extra load, (2) add beams to support the intermediate weight and (3) dig down as the beams will take over some headroom. This is what they say when they mean "Rail Viaduct Risk". And my guess is that it'll take quite a lot of money when drawings are done.
And likewise the operating costs are way too close together. By reducing peak load on the streetcar there needs to be fewer streetcars running the entire length of Queens Quay (East and West). About 1/2 as frequent. How does this not reduce cost?
My cynical self is that someone at City Hall/Davisville already knows this. But has hidden this information so it does not factor into the decision (just like Sheppard). Why is no paper nor the Board of the TTC not asking these questions?