When you configure OE using bitbake, it appears that a python function called get_kernelversion() is called to determine the kernel version. This function looks for some headers in your kernel source tree, specifically utsrelease.h. What I wanted is to override this kernel version (in my case, my ubuntu system is 2.6.32) with one that has an RT patch available (e.g., 2.6.29), and build my kernel for that version.
I'm not sure why the kernel version built by bitbake is coupled to the kernel version of the host. Seems like they should be separate.
I posted about this here. A response came in several hours later (which you can read by clicking the link). After making the changes that were suggested, I did:
bitbake virtual/kernel -c clean
bitbake virtual/kernel -c configure
bitbake virtual/kernel -c compile
Was able to get a 2.6.29 uImage file after following the above steps. Next step is to test it.