you are correct... it's all about the OS, not the hardware.
(another insight is that UNIX has been running on 64bit machines for years (over 10 years...eg, Alpha chip, PA-RISC, SPARC) and the UNIX time issue has still continued)
I think an all-64-bit OS X will probably solve this. It could be a Jobs keynote..."we made it through 2000 with no problems at all. Now watch as I advance the new Mac OS X 10.6 to 2038."