First of all, the cost of subway won't be enough to pay for 3 light rail lines. The rule-of-thumb ratio is about 1:4 (4 km of light rail for 1 km of subway). The 3-stop subway will be 7.5 km long, that can cover about 30 km of light rail, but not 40 km.
The apples to apples comparison would be two light rail lines, say SLRT plus Eglinton East, vs the subway. If we have only 2 LRT lines, the access argument gets weakened. Instead of 1 in 6 residents within walking distance of a light rail stop, we will have 1 in 9, or 11%.
If 23% of Scarborough transit riders travel to DT, then roughly half of them will benefit from the subway extension. Same 11% of all riders.
How much time will be saved? That will vary from one trip to another, but the range is similar. The subway extension eliminates the transfer at Kennedy: let's say 5 min walking from one vehicle to another, plus 2-3 min waiting for the next train. Plus, the subway will be 3-4 min faster because it will have fewer stops. Total saving should be 10-12 min each way.
LRT? If the length of a typical LRT trip is 10 km, that will take 26 min at 23 kph. On a bus (17 kph), the same trip would take 35 min. Total saving is about same, 9 or perhaps 10 min.
However, there is one category where subway definitely wins: compatibility with the future transit enhancements. A subway in the McCowan corridor doesn't in any way preclude EE LRT, or other light rail lines for that matter. EE LRT may be delayed by a few years, but it stays on the books, and will likely catch the next funding train.
On the contrary, if SLRT is built now instead of the subway, it will not be replaced with a subway in any foreseeable future.