Changing my netboot preseed configuration from "d-i pkgsel/upgrade select full-upgrade" to "d-i pkgsel/upgrade select none" was enough to get around this problem.
Hopefully the installation process still apply the security updates. It seems to do it later in time so it's probably why it doesn't fall into this very specific initrd.img symlink race condition case anymore.
Changing my netboot preseed configuration from "d-i pkgsel/upgrade select full-upgrade" to "d-i pkgsel/upgrade select none" was enough to get around this problem.
Hopefully the installation process still apply the security updates. It seems to do it later in time so it's probably why it doesn't fall into this very specific initrd.img symlink race condition case anymore.