Now, it's easy to miss, but in fact the README does not say you shouldn't use /usr/src. It does say not to use /usr/src/linux, a directory that is not present on Debian systems. Actually, on a default Debian system /usr/src is empty.Do NOT use the /usr/src/linux area! This area has a (usually incomplete) set of kernel headers that are used by the library header files. They should match the library, and not get messed up by whatever the kernel-du-jour happens to be.
When you install a kernel-source via apt-get it is put automatically in /usr/src and when you unpack it it creates /usr/src/linux-source-2.6.x.x. Exactly the same as if you unpacked in, say, ~/kernel. It would then create ~/kernel/linux-source-2.6.x.x
The reason for using /usr/src is mostly that it is a convention, and also that it is the directory where apt actually places it. And although it's true that you can build the kernel wherever you want it does no harm doing it under /usr/src. By doing so you are creating a unique directory for your new kernel source anyway when you unpack it.
So in conclusion; I see no logical reason not to use /usr/src on a Debian system.
If someone can proove me wrong please do. It's really about time this issue gets settled. Also, if the above is wrong the Debian developers needs to change the behaviour of the source in the repositories.
Tina