Once again you can fix this of course locally very easy, but you can't write sth. like that in the ebuild, because the ebuild works as it should (it writes the libGL.so.1.2 to /usr/lib/opengl/ati/lib and then symlinks libGL.so.1 and libGL.so to it in that directory). Because there are seperate opengl impelementations (xorg-x11 and ati) you need a programm to select the right one and that is eselect, which sets the symlink to /usr/lib. The ebuild should not do that, so there is nothing from the side of the ebuild, that could be done.
as for the soname issue, i don't really think that this is a real problem since it is fixed with a simple symlink. of course that should be fixed in the next release and i think that ati would correct that feature by next month's release. for now just add the symlink part in the ebuild and you'll have it working.