Something like this:
View attachment 700766
At ~4.4 km, you are probably looking at about $1 billion to tunnel it
as per latest cost comparables and $2-3 billion for fitout and a mined terminal station at Union. If you are willing to cut travel speeds you could probably reduce the tunnel length to something closer to 3km.
Expensive, but it would give ALTO completely separate (i.e. reliable) operations in and out of Toronto and would let trains get from Union to the edge of the City, assuming an average speed of 150km/h between Union and Markham, in about 11 minutes. Doing the Union-Kennedy-Agincourt route is probably looking at more like 21-22 minutes.