Again these issues are easily dealt with a build service where optimized packages can be built for pretty much any arch. openSUSE's public build service for example is pretty much next day releases when dealing with items such as X11, kernel, alsa, gcc and the various other quick changing projects.
Depends. If the machines have similar hardware then the configs are the same as well. But even if they are not, then you just make a general stage4 and put it everywhere. Like this you don't get advantage over tthe binary distros, but still you can have as a lean system you want, which is a valuable advantage as well. but still as smitty3268 pointed, with gcc-4.4 you can use march=native, which helps a lot.
Also, the rolling nature of Gentoo, helps to keep every server and client moden for ever, unlike the conventional distros.
But for sure Gentoo isn't a distro which can be used in your machines in dt time unlike OpenSUSE etc.
That's the thing, I don't know where you see these huge differences. As far as the game tests in the above article goes again this can be done on any distro if you wish to compile from scratch or setup a build service to do so automatically. At work for example I run a build server there and separate packages are built for pentium 4, amd64, ia32e and ppc (distributed among various machines, some old workstations to newer machines that are just not used alot using icecream) . When a update comes out from the update service (or a upgrade version from watched projects) it goes out and retrieves the src rpm and builds updates for all of them utilizing the specific optimizations. Set and forget.
True, but why we see so large differences in the benchmarks between binary distros even if they use the same DE, graphics and kernel?