There are indeed treaties - which from my understanding give pretty clear direction that the Haudenosaunee (or really, the Mississaugas of the New Credit) forfeited lands in the GTA to the Crown.
The reserve and lands along the Grand River are generally a bit more disputed, as the treaty isn't as clear (the reserve as originally defined in the initial treaties was land on both sides of the Grand River for most of it's length, later shrunk down to just Six Nations), but the treaties covering the GTA are not that disputed. Or at least, this is the first time I've heard of an indigenous group disputing title holding on the lands.
I think (i may be wrong) that the Haudenosaunee are claiming here that the lands are their "traditional territories" and they have a right to compensation based on that, regardless of what a treaty from the 18th century might say. And that's the overreach. They have a right to consultation and oversight on the matter, as Metrolinx has done, but not to compensation.
Highway 69 is a distinctly different issue as it actually runs through a current day indigenous reserve. Same thing with the Calgary Ring Road, it runs directly beside the Tsuut′ina reserve. It's not running solely on ceded territory like Metrolinx's Lakeshore West line.
The problem lies in this quote:
The problem is that Lakeshore West does not run through Indigenous lands or their territories. It runs through their
traditional territories, but those are covered by those old treaties from the late 18th century and early 19th century showing the lands being ceded to the crown. The last known disputes on the Toronto purchase were settled in 2010:
en.wikipedia.org