EDIT: I figured out that for whatever reason, the Flathub version just doesn’t function properly. When I install the tarball from Yubico’s website, the executable DOES work right,
It looks like because the sandbox of Flatpak prevent the program access the unix domain socket of pcscd.
but I can’t seem to figure out how to make the .desktop file install into the programs list.
There is a document on Arch Wiki.
Actually some vendors implements NTFS driver in their UEFI as well.