This clause allows the federal government to collect tolls on the new bridge, but the federal government has yet to provide a solid business case justifying these tolls. The proposed tolls are opposed by the City of Montreal because of how they will divert traffic and contribute to greater congestion, thereby hurting the region's economy. We've proposed five amendments—and as you've rightly pointed out they are consequential—to remove specific provisions allowing the federal government to establish and collect tolls on the new bridge.
It's pretty simple. Unless there's a business case that's been made, which it hasn't, there's no basis for getting an amendment to a bill.