The scripts in /usr/lib/kernel/install.d are used by systemd's kernel-install command. man 8 kernel-install kernel-install will execute the files located in the directory /usr/lib/kernel/install.d/ and the local administration directory /etc/kernel/install.d/. I've used the kernel-install command to generate the initramfs and to add a boot loader entry for gummiboot. This worked fine with dracut-041. Please consider dropping the 041-r1-0004-Don-t-install-scripts-in-kernel-instal patch.
Ah, it's systemd-specific... :-)
Thanks! +*dracut-041-r2 (28 Mar 2015) + + 28 Mar 2015; Amadeusz Żołnowski <aidecoe@gentoo.org> -dracut-041-r1.ebuild, + +dracut-041-r2.ebuild, + -files/041-r1-0001-Use-the-same-paths-in-dracut.sh-as-tho.patch, + +files/041-r2-0001-Use-the-same-paths-in-dracut.sh-as-tho.patch, + -files/041-r1-0002-Install-dracut-install-and-skipcpio-in.patch, + +files/041-r2-0002-Install-dracut-install-and-skipcpio-in.patch, + -files/041-r1-0003-Take-into-account-lib64-dirs-when-dete.patch, + +files/041-r2-0003-Take-into-account-lib64-dirs-when-dete.patch, + -files/041-r1-0004-Don-t-install-scripts-in-kernel-instal.patch: + Don't remove kernel/install.d scripts if systemd is enabled. Fix bug #544558. +