One of the motivations for UsrMerge is to have all read-only parts of
the operating system in /usr. The kernel packages install files in /boot
though which isn't in line with that idea.
Having the kernel installed via rpm in /boot also causes issues with eg
snapshots if /boot is on a separate partition.
So it make sense to store the rpm provided parts of the kernel packages where
the rest of the OS is and manage /boot separately.

Looking at Fedora they install files like vmlinuz that used to be named
/boot/$name-$kver as (/usr)/lib/modules/$kver/$name instead. They
include /boot/$name-$kver as %ghost.