I found this over at the O'Reiley book on Kernel building. Seems relevant here:
I think I'm going to listen to this stern directions, as I don't see why it is necessary to build the kernel in such a special location. I think mine shall go in my home directory unless somebody tells me that's a stupid idea (it isn't, right?).The kernel source code should also never be placed in the /usr/src/linux/ directory,
as that is the location of the kernel that the system libraries were built
against, not your newcustom kernel. Do not do any kernel development under
the /usr/src/ directory tree at all, but only in a local user directory where nothing
bad can happen to the system.