Considering how block-to-block copies work, it would be hard for any program invoking a block-to-block copy to mess up. This is like a photograph, and getting hard links wrong would be like a doctored photograph. Disk Utility and CCC are undoubtedly making the same underlying system call for this, which doesn't doctor the photo. One doesn't need to assume good will here, just laziness; it would require completely independent code to go in and doctor a block-to-block copy.

Nevertheless, Disk Utility does its very best to mess up what it can, restoring in block-to-block mode. It may take a faithful photograph, but it screws up the caption with a vengeance. It changes ownership of the volume itself, and re-enables in horror-movie fashion the dreaded "Ignore ownership" setting that you thought you could forget about after fuming while taking care of this when you first formatted the target drive. (PLEASE provide Apple with feedback that you do not appreciate any aspect of the "Ignore ownership" default.)

Restoring in file mode, Disk Utility is worse than a Finder copy, letting you authenticate so you can peer into files that aren't yours, then changing all permissions. This is truly unfortunate, as file mode would sometimes be desirable if it worked, e.g. to defragment a drive.

To insure block-to-block mode it must be possible to unmount both the source and target volumes (practice from within Disk Utility before the restore, as there will be no confirmation before DU does it the dumb way if it can't unmount), and be sure to check "erase" as part of the restore.

Google "backup bouncer" for an education on what does and does not get copied correctly by various programs. While we're busy exchanging hearsay, that program does empirical science for you, on your own system with whatever versions of programs you actually have installed.

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