Does anyone knows if the Borderlands bundle on the Humble store comes with seperate keys?

General rule of thumb:
If it's a package you can find on Steam, then it's usually that (single key) package.
If it's a combination you can't find on Steam, then it's likely separate keys.

Best answer I can offer until someone who actually bought what you're mentioning can reply.
A link may be helpful for them to be able to answer you properly. :)

Humble Support may be terribly delayed for a lot of people in responses of late, but from what I've seen they're still excellent overall. May just wanna send them a poke over it, to be sure.

email humble bundle support and ask.
they'll answer your question.

Yup, it's all separate keys if you mean the handsome collection. One key for BL2 GOTY, 1 for Pre-sequal, and one for pre- season pass.

thanks everybody!