Backgrounds are meant to be what you did before you became an adventurer, not a mechanic system for giving you abilities.
The most important question to ask about your background is what changed? Why did you stop doing whatever your background describes and start adventuring? — Player’s Basic Rules, pg 36.
I am not sure that Dragonmarks work as a background.
But, a Dragonmark house member background could give you benefits with that house, similar to how some of the other backgrounds give benefits when visiting a temple or military area. You could get discounts or service with the house. Really the most powerful part of being a member of a dragonmarked house. Also, not all members of the house have a dragonmarked manifested ( I think its like 80% don't), they are just part of the bloodline.
I may want to be a former House Cannith magewright as a background but not have a dragonmark, I also might want a dragonmark but be a solider in the last war before I manifested my mark.
I do believe that "Creativity" can go a long way into re-flavoring your abilities. Maybe you are a wild chaos sorcerer and all your abilities are because of your aberrant dragonmark. You dont need a "mechanic" to say you have a mark, its just how you are describing how you got your sorcerer abilities.
I do think the Feat system is a good place to start or at least how you "pay" for feats. I think an optional Eberron rule could allow for a player to trade in an ability score boost for a dragonmark feat. I could also see Dragonmarked being a subrace or subclass. Trade a feature for a feature.
I also feel that psionics fits into the feat system.
Warforged where in the playtest at one point +1 str +1 con med 30 speed, I think they got +1 ac and got trance and immunity to disease.
I think all characters should get a feat at first level to be honest, but maybe Eberron characters start off at level 4