The initrd is actually generated when building the ostree and not on the target system. Because 98ostree/module-setup.sh is present when generating the ostree, the system initrd is created with the right hooks to do the ostree pivot root magic. And that’s the initrd that is used in /boot.
sudo md5sum /boot/ostree/fedora-workstation-2337b6475f858eb29167353cee4705c0f5f49ab8550ffe37788d4697f3cb3004/initramfs-4.19.4-300.fc29.x86_64.img /usr/lib/modules/`uname -r`/initramfs.img
c9c8afd6f55a1294a0550a4b292435d9 /boot/ostree/fedora-workstation-2337b6475f858eb29167353cee4705c0f5f49ab8550ffe37788d4697f3cb3004/initramfs-4.19.4-300.fc29.x86_64.img
c9c8afd6f55a1294a0550a4b292435d9 /usr/lib/modules/4.19.4-300.fc29.x86_64/initramfs.img
I’m not sure if that answers your question or not.