I don't know why you're getting so hung up over this. Everything leading up to this has been lead by the City of Toronto in consultation with parter agencies, including TTC and Meteolinx. See
http://reliefline.ca/the-project/the-process
If you've been to the public meetings, you'll see that the staff there are TTC, City of Toronto staff with some staff from contacted firms. It's quite a stretch to say that this has been lead by Metrolinx, when they seemingly haven't done any major work since the YRNS release last July. If you ask Metrolinx for more information about the RL planing process, they send you straight back to the City.
Could that change in the future? Absolutely. It did change for the Crosstown. But the province hasn't indicated any desire to take over this file.
Ultimately though, this really doesn't matter. I don't understand why some people get hung up over these things.