This article is hugely biased, misleading, and not altogether accurate.
Statements like "Michaëlle Jean, in her role as governor general, was the first to witness survivor accounts of the Truth and Reconciliation Commission. David Johnston was one of the last" imply things that aren't true. You read that and think there have been a long line of Governor Generals, starting with Micheälle Jean and continuing on to the present (with Johnston falling somewhere near the present), witnessing this commission. Except their hasn't; Johnston is the current GG, and Jean is his immediate predecessor.
Aboriginal affairs falls under federal jurisdiction, and the federal government acts on behalf of the Crown in all matters relating to Aboriginals in Canada - just like they act on behalf of the Crown on all matters relating to national defence, or currency, or any other federal matter. The Queen or GG has the same responsibilities here that they have to any other federal matter.
Treaties in Canada were signed before confederation by various officials depending on the territory/who was in charge (i.e. in BC, the Douglas treaties were signed by James Douglas, then Governor of the Colony of Victoria). Shortly after Confederation, the federal government signed the Numbered treaties (11 between 1871 and 1921), then halted the treaty process (because of purely racist reasoning), with a focus on eradication of Canada's Aboriginal population, until the 1970s, when the federal government began what is a rather painstaking slow modern treaty process that attempts to actually bridge some reconciliation between Canada and the Aboriginals. One of the major modern treaties, the Nisga'a Final Agreement, was signed in 1998 by several important Nisga'a leaders, the then-Premier of BC, and the then Minister of Indian Affairs and Northern Development - not the Lieutenant Governor of BC, or the Governor General of Canada, or the Queen.