Staff estimated the subway would save five minutes off travel times between STC and Kennedy due to the elimination of station in between. And if you're travelling past Kennedy, the elimination of the transfer saves up to 3 more minutes, so that's 8 minutes in total for this subset of riders. Since the numbers are in comparison to the existing RT, not the LRT plan, they don't account for the riders on Lawrence and Northeast Scarborough who who will see their commute time increased compared to the LRT.
These numbers are not imaginary or created out of thin air like yours. They were produced by knowledgeable people based on their analysis of the proposed alignment. Variables like how quickly a vehicle can make a trip without stopping (versus how quickly the current vehicles do make the trip) are fairly well understood by those doing the planning. So if you wish to reject their findings in favour of your own fictitious version of reality, and just assume that the real savings are actually double because somehow you know better, then I can't help you.