The difference is that in 3.5 and 4e the dragonmark progression was largely orthogonal to your class progression; you strengthened your dragonmark by taking feats that you got based purely on level, not on class selection. Granted, some classes got a few extra feats based on their class progression in 3.5, and PrCs like Dragonmark Heir and Heir of Syberis let you turn class levels into further dragonmark progression, so it wasn't a completely separate progression, even then. But I can see where it could cause people some dissonance, especially if they play with class being a strong presence in the game fiction.