The ebuild for pecl-gnupg has this dependency: <app-crypt/gnupg-2 I can't see anything in the package's docs docs that indicate that it depends on an ancient gpg version, so I guess this is wrong. pecl-gnupg is a binding for gpgme, so it shouldn't care what underlying gpg version is there anyway. I can only guess that there is some confusion with the version numbers: pecl-gnupg itself is currently at version 1.4, which aligns with the "classic" gpg 1.4.
From the README recently updated in 1.4.0: The extension supports only gnupg version 1 and the version 2 is not currently supported. It should be fixed in the extension version 1.5.