Adding costs due to adding inefficiency in the supply chain is definitely a bad thing, since you could easily achieve the exact same outcome with a tax instead.
This is true, but if new taxes are politically untenable (which, in the current US political environment, they definitely are), the choice isn't between inefficiency and a tax, it's between inefficiency and the status quo. Politics is the art of the possible.
Sure, but you should also just not give permits when the project is dangerous (which was what multiple agencies and courts had suggested in this case but one of the last three administrations was trying to overrule them)