The response you describe from the store manager was excellent, in my opinion. They clearly accepted and shouldered responsibility:
1) New HDD - this means you are able to start using the Mac as soon as possible. - Free repair that you would otherwise have paid for.
2) You keep the old drive - you're able to pursue data recovery without impediment.
3) An offer to pay recovery costs (my guess is they may offer to share recovery costs if they're too high) - this is a very rare offer.
Anything beyond that goes from "make good" to "punitive damages." If you take the punitive damages path, "make good" will be withdrawn, Apple retreats behind the fine print of the repair contract, and you take your chances on success.
As for the reminder (from Apple) that they're not responsible for data loss... That's not BS, that's a statement of a policy and self-preservation that you'll find at any repair shop. If these businesses had to be responsible for the contents of every computer loaded with "priceless" personal and/or business data, they'd need the equivalent of U.S. medical malpractice insurance. And then there's the fine legal point, "How do you prove the value of something that no longer exists, or maybe never existed?" And in terms of privacy of customer data... the safest thing for a repair shop to do is to erase everything as soon as the equipment enters the shop.
You've had enough lectures on backups, but here goes. A key point here is that backups weren't made when they should have, even though you intended to make them. Whatever you do going forward, be sure that backups are not voluntary. (That's why I prefer iCloud backups of iOS devices to iTunes backups - automated backup trumps, "backup when you remember to connect to iTunes" every day of the week.) Cheapest and easiest, just use Time Machine, and leave the backup drive(s) connected at all times. And if the materials truly are priceless, then a second, off-premises backup is a good idea.
And please, do a full backup of the computer, not just the photos, not just your business documents. As Joni Mitchell wrote (and sang), "Don't it always seem to go that you don't know what you've got 'til it's gone."