The Charter (including the notwithstanding clause) do not apply here but the constitution does.
s 91 provides
s 92 provides
My reading is that if a pipeline is inside a province and doesn't extend outside of it then the province controls but if the pipeline connects several provinces or simply transits a province from one to another through a third then the Feds are in charge. The responsible agency is the
Canada Energy Regulator.
This is far from my area of expertise, but I think that a Federal government, with the political will, could make it happen.