The DLC bundle is essentially the Steam "Season Pass" that included all the expansions released for the board game along with several single characters. There is a special exception for those who got the Season Pass very early on, as it stated at that time that it would include all future DLC.
The three digital only (Realm of Souls, Ancient Beasts and Clockwork Kingdom) expansions and the Legendary decks were added after Nomad finished releasing the physical expansions. Same with the characters that aren't included in the DLC bundle except the Shaman. The Shaman was created for a charity while Nomad were still working on the board game expansions, and since it was made for a charity it was never included in the Season Pass.
It's also worth noting that Nomad have a IMO fair approach to the DLC. In a multiplayer session a DLC is available if it is owned by just one of the players in the lobby. Additionally, as long as you own the base game and create a Nomad account, you can sync what DLC you own across the various platforms the game is released on as long as you own the base game on that platform (PC, iOS & Android).