The new kernel wouldn't be flashed on the NAND, it'll be kept as a separate option in u-boot to boot. We won't be dealing with the 2MB flash size limit.
*Note, you can take out the UBIFS and cramfs drivers which are inlined into the kernel. Why do we have those when we intend to boot into eMMC?
Furthermore, we can simply tweak bootmenu.scr to have the eMMC boot system as default. No biggie.