I'm well aware of section 1498:
"Whenever an invention described in and covered by
a patent of the United States is used or manufactured
by or for the United States without license of the owner thereof or lawful right to use or manufacture the same, the owner’s remedy shall be by action against the United States in the United States Court of Federal Claims for the recovery of his reasonable and entire compensation for such use and manufacture."
www.law.cornell.edu
The main thing 1498 does is strip a patent owner from the ability to file for an injunction against the U.S. government.
Also, the U.S. government does not "confiscate" patents under section 1498. The government does not obtain ownership rights in a patent so it cannot license others or sue others. The party that owns a patent retains the ability to enforce it's patents against others even if the government is successful in a section 1498 action.
Under the proposed waiver of the TRIPS foreign countries want to make the vaccines in their countries. Section 1498 does not apply because the activities in foreign countries are not covered by US patents and the activities would not be conducted by the US government.
The TRIPS agreement incorporates the Paris Convention. Basically, the Paris Convention says that all countries who sign the agreement must permit inventors from foreign countries to apply for patents in their country. If a company applies for a patent in it's home country, it still needs to file patent applications in foreign countries if it wants patent protection in the foreign countries.
Keep in mind that each country has it's own laws governing activities in that country, but a country can't (for the most part) pass a law that controls activity in other countries. The process for treaty implementation varies somewhat from country to country, but treaties basically say "By signing this agreement we agree to pass laws in our country consistent with the agreement."