What exactly was the option letting you select a custom initrd? This doesn't seem to be a question that comes from the initramfs-tools package.
After reinstall, did you use the same syntax in /etc/crypttab? I think the issue here is that the cryptdisks-udev job handles UUID=, LABEL=, or /dev/sd* as source devices, but is not configured to handle /dev/disk/by-id. So this device will only be brought up if it's caught by the cryptdisks-enable catch-all job, which is racy.
What exactly was the option letting you select a custom initrd? This doesn't seem to be a question that comes from the initramfs-tools package.
After reinstall, did you use the same syntax in /etc/crypttab? I think the issue here is that the cryptdisks-udev job handles UUID=, LABEL=, or /dev/sd* as source devices, but is not configured to handle /dev/disk/by-id. So this device will only be brought up if it's caught by the cryptdisks-enable catch-all job, which is racy.