Why is Serius Sam 3: BFE Deluxe in a bundle list?

Because someone was smart enough to create SS3 deluxe giveaway and just send SS3 key from bundle and a separate Deluxe upgrade. Probably it pissed off some elitist who is against "contribution farming". But then why Collection is not a bundle? Half of SS games were in some bundles, just add 2 DLCs and HD versions and there you have a complete collection.

Basically what Arukardo said was actually happening. If you had a spare key from the bundle you only had to pay $2 to get a full $50 contribution value from it, bypassing the bundle limitations.