I don't think the fact that mixing chakra natures requires a bloodline limit is meant to imply that all bloodline limits involve mixing chakra natures. There is more to the ninja world than just elemental chakra manipulation so it wouldn't make sense for all of the special clan-based techniques in the ninja world to be bound to only a subset.

Stuff like the super bones and the doujutsu we've seen probably don't have any sort of chakra type requirements. Instead I think they are genetic abnormalities in otherwise normal, chakra producing, people that can make use of regular chakra to do abnormal things.