The point is that Native Client binaries are arch-specific. You only get the archs that you build for: If someone puts up a NaCl site with only x86, it won't work anywhere else. This is a horrible thing for the web.
Yes, you can build for more than one arch. But if you have x86 and x86_64, you are missing ARM. If you add ARM, you are missing PowerPC (consoles) and MIPS (some phones). If you add those, you are still missing new archs that will be invented later.
For this reason Google is working on PNaCl - but it has other issues.
You need to make it work for it.
It's not a very good analogy because parts are portable, but good enough for me:
I can recompile my C program for arm. Doesn't make the x86 binary run.
Yes, you can build for more than one arch. But if you have x86 and x86_64, you are missing ARM. If you add ARM, you are missing PowerPC (consoles) and MIPS (some phones). If you add those, you are still missing new archs that will be invented later.
For this reason Google is working on PNaCl - but it has other issues.