I expected to get this working "out-of-box".

Did you do a  "bitbake -e <your kernel recipe>" ? and then look at
the SRC_URI ? That will tell us if for some reason the beagle layer's
defconfig is on there twice.

Why config fragments did not worked too?

recipes must inherit linux-yocto to get that support, since it is
optional and not something we force on all kernel recipes. So if you
want fragment support, creating your own kernel recipe, based on the
one in the layers you are using, which inherits linux-yocto is one
route to take.