In a setup where /boot is encrypted and placed onto completely separate encrypted disk, and keyfiles are used in crypttab, runit (03-filesystems.sh) tries to check the /boot partition for a keyfile but fails due to it not being mounted by dracut(initramfs) or anything else.
The cryptdevice of /boot partition is already opened in previous booting steps (I assume by grub), it's just isn't mounted yet, at the very end of 03-filesystems it reads fstab and mounts everything properly.
The end result is that I can see warnings during boot about "Failed to open key file.", but otherwise boot ends and mounts everything just fine.
I've added a couple of lsblk checks before "Activating encrypted devices" and after it, to show the point, and also show my configuration in this video:
https://fastupload.co/1097693