Where do the concept of the favor, bounty and doctrine [blessing] cards come from? as far as I know they are not in the physical card game.

All of the Rare, Epic and Legendary cards that you find in Treasure Chests are unique to the digital version. I develop the cards with review and assistance from the original card game designers at Lone Shark Games and at Paizo. So far Favors allow you to stack blessings on a check, Bounties are all about Boons, and Doctrines focus on specific sets of skills. There are some new blessing sets on the way that are all about taking advantage of your placement on the map. For Example, you will start to see "Unity" blessings that give a big boost to specific checks when played on another character at your location.