ref-manual: add missing features

Add missing IMAGE_FEATURES, DISTRO_FEATURES and MACHINE_FEATURES items.
Additionally, add a note that DISTRO_FEATURES doesn't have any impact on
the kernel configuration so that users are aware they have to take care
of that as well. (I thought the same was true of MACHINE_FEATURES, but
it seems we have a couple of isolated cases where that will adjust the
kernel configuration - few enough that I suspect they might have slipped
in and thus probably shouldn't be documented yet.)

(From yocto-docs rev: 488a5896feefd6d0dbc197e7cc431b4d23085104)

Signed-off-by: Paul Eggleton <paul.eggleton@microsoft.com>
Signed-off-by: Richard Purdie <richard.purdie@linuxfoundation.org>

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