I looked at a current publication in PNAS and they are still parenthetical? I do note in their instructions to authors, that the output style for PNAS was updated in April 2019 and I see that an updated version is available to download from Endnote’s style pages. But it has the citation template parenthetical and not superscripted.
You would need to edit the output style “citation template” to remove the parentheses and superscript the numbers and save it to a new name (and change the endnote output style in the manuscript in word). But I see no evidence of the instructions for PNAS that you describe.