In fact, they don't.
In terms of provincial agreement, the provinces are indeed consulted for the designation of projects of national interest. However, it's only a consultation. Perhaps the people who drafted the bill didn't quite capture the Prime Minister's intention. If the provinces are consulted for the designation of bills, their consent isn't required.
Moreover, this isn't the first time that federal legislation has attempted to provide a single assessment for a single project. It's a good idea to have joint assessments involving people from the federal and provincial levels. However, the idea of a federal project or assessment doesn't fit in with Canadian federalism. A number of projects that could be affected by this legislation fall under exclusive provincial jurisdiction. The environmental aspects related to federal jurisdictions fall within the purview of the federal Parliament, while the environmental impact of projects under provincial jurisdiction lies with the provinces. However, the current bill seems to want to replace provincial assessments. According to constitutional law, this isn't possible.