The ebuilds still use paxctl and that don't have any support for the xattr pax markings. Depend should be change to sys-apps/elfix that have the xattr support.
Call to paxctl should be change to paxmark.sh and no need to pass C to the pax-utils eclass or paxmark.sh for it should use C when marking, if the first marking fail. The paxmark.sh is a bash script version of the pax-utils.eclass.
More of the java vm may be affected to.
I was just thinking the same while looking at the existing PaX code. I'll be updating this in the ebuilds (at least in the overlay) now I'm on a PaX XT-only system myself. Thanks for making me aware of paxmark.sh.
Released in 1.13.2, updated ebuild in overlay: http://bit.ly/1f0BhnC
Released in 2.3.14 & 2.4.6, ebuild in overlay: http://bit.ly/1rKqaoa
it should be fixed with the latest bump.
Marking as FIXED.