They’re just referencing the commerce clause. Can the commerce clause supercede the bill of rights?

Commerce clause has been used for all sorts of 2A regulations.

The federal government regulates firearms under the commerce clause the same whey they regulate pharmaceuticals under the commerce clause. The difference is they can outright prohibit marijuana and not rifles because the latter prohibition would violate the second amendment.

The commerce clause doesn't override the second amendment (or any other part of the bill of rights), there are only cases where a particular amendment was found not to apply.

What you're looking for is emergency powers, but they're not actually in the constitution. In practice what has happened is that Presidents do whatever thing in an emergency and then get sued over it after, and typically lose, but by then it's years later and whatever temporary measures they ordered in the middle of the emergency are long since discontinued.

It's kind of a kludge, but it also kind of works, because it keeps the emergency measures from extending longer than it takes for the courts to catch up to it, and also gives the victims of rights violations the ability to get compensated after the fact for being done wrong in the midst of a big mess.

If you're thinking of the gun free school zone law, I don't think it quite supports your point. I believe the Commerce Clause was used to justify federal regulation of gun purchases/ownership, as opposed to it having to be a state law. It was not used (I believe) in any way to abrogate the rights afforded by the Second Amendment. I could be wrong — I never practiced law in this area — but I can't remember ever hearing about the Commerce Clause being used as a limitation on the Second Amendment. That is effectively what would be required here.

The Federal government requires local cooperation to enforce any such orders, they operate at the pleasure of local authorities. This limitation on Federal power shows up routinely in other matters when local authorities disagree with Federal enforcement actions. Hence the reference to CBP and the Coast Guard, which do have authority to enforce such things at points of entry into the country.

There are also strong restrictions on the scope of quarantine orders that would be allowed to circumvent due process in emergencies.