Okay, so here is the response I got from Steam support regarding the Torchlight II bundle:

Quote: Hello, Thank you for contacting Steam Support. Thank you for taking the time to report this issue. Currently, the missing subscription is appearing about 6 - 48 hours after purchase. We are aware of the problem and are investigating the issue further. We thank you for continued patience. Please exit completely out of Steam then log back into Steam to re-test the issue. If you have any further questions, please let us know - we will be happy to assist you.

The missing copy did show up for me when I started up Steam today, so I think it's fine to buy- there's just a chance that you'll have to wait several hours for one of your giftable copies to show up.