Why would Apple do that?
The problem is compatibility with third-party drivers. Some programs are so deeply intertwined with the OS that they reach deeply into its bowels and modify its core, the kernel - these drivers are called kernel extensions (or kext).
Rule
A 32-bit processor can only run 32-bit stuff.
A 64-bit processor can run 32-bit and 64-bit stuff.
(stuff can be system, kernel, applications, drivers, etc)
So you need a 64-bit processor to run 64-bit anything
On a 64-bit processor:
A 32-bit Kernel can run both 32 and 64 bit applications.
A 64-bit Kernel can run both 32 and 64 bit applications.
A 32-bit Kernel can load only 32-bit kexts (kernel extensions).
A 64-bit Kernel can load only 64-bit kexts (kernel extensions).
If a program uses a 32-bit kernel extension (like the PC emulator VMware Fusion) then that extension will not run in a 64-bit kernel. So until they update their kext the program will not run if you start the kernel as 64-bit. However the program will run fine if the kernel stays 32-bit, even if the application itself is 64-bit)
The ability to start up with a 64-bit kernel (by holding 6 and 4 while booting) is meant for developer so they can start developing 64-bit kernel extensions. The average user never really 'needs' to be in 64-bit kernel - in fact, you wouldn't want to have a problem with your 32-bit kernel extension, would you?
So Apple leaves the kernel at 32-bit for now but includes the ability to start the kernel in 64-bit mode.
Unlike how other vendors have approached 64-bitness Apple's implementation will just work without worrying about whether you have 64-bit everything or not - just install and go