I think the ebuild of dev-php/PEAR-Net_FTP should have a RDEPEND for dev-lang/php[ftp] Reproducible: Always
It looks like that ebuild uses the depend.php eclass which should alert the user to rebuild php with the ftp use flag. You are right that it doesn't automatically pull in the dependency with the RDEPEND including dev-lang/php[ftp]. I'm not sure what the developers think of this but with at least EAPI=3 we should be able to change this behavior to work as we would expect? Can someone with a little more knowledge on how the depend classes work explain why they can't inject RDEPEND values or why we use them rather than specifying the RDEPEND values in the ebuilds?
We're already planing to get rid of depend.php, but the sheer amount of packages means we're unable to check and convert every one of them. That said, I've fixed this package now. Thanks for helping.