Before negotiations even start, the federal government has already consulted with first nations and gotten their perspectives and their consent on things like the annex list of what's a tradeable good. What should be on there? Most first nations would say water shouldn't be a tradeable good, so these are the kinds of things that can be dealt with long before you get to the negotiating table. That way you're not in a position of going back and forth.
The other thing is making sure you have consent or opt-outs for very specific regions, and they're going to differ. Different regions have different concerns. Some are fish, some are timber, and some are land. At a bare minimum, each of these has to go through an indigenous rights analysis and a gender-based analysis as part of that consultation process.
Then you're far more likely to get agreement, fewer legal challenges, and a trade agreement that respects a whole host of issues addressed by other groups. Indigenous peoples raise environmental issues, workers' rights, and safety. All of those things would be addressed and go a long way to addressing all of the social impacts of free trade agreements. As we know, NAFTA has been the worst for indigenous peoples in Canada, the United States, and Mexico.