No, they're saying an improved + diverted Milton line would *be* the subway, only faster and cheaper.
Since no one is going from Kipling to Kennedy (they're going from beyond Kipling to beyond Kennedy if they go that far at all), they can take improved GO trains...which conveniently stop at both places already.
But nowhere near the level of frequency or reliability required to consider taking the GO a viable option. By the time one gets to the Milton line, awaits a train, gets off at Union, awaits a connecting Stoufville train, and takes that to Kennedy one already would long have arrived at Kennedy via the subway and guess what it'd only cost one fare which gets onto a connecting bus/RT train for free.
Why should this new 'subway' be incorporated onto the Milton line? The amount of local stops that would have to be added on to the GO service, would make it completely inconvenient for long-distance commuters (from Meadowvale and Milton/Halton Hills). What I'm inferring instead is a completely independent service most likely operated by the TTC to alott seamless transfer onto other TTC vehicles once in Toronto. It would most likely have stops at:
Union, Skydome, Fort York, Strachan, Exhibition, Queen West, Brockton, Bloor/Dundas, Annette, Junction (Keele or Runnymede but not both), Jane/Dundas, Kingsway Mills, Etobicoke Centre (Islington), Kipling, Shorncliffe, West Mall (Sherway interchange), Dixie, Tomken, Cawthra, Cooksville, midblock between Central Pkwy and Burnhamthrope, and finally Square One terminal.
You could also make it express east of Kipling omitting those intermediate stops but adding them in was to offer some DRL local practicality to the line.