So it sounds like it is the baserunner's responsibility to pick the "unused" bag in the first two examples (throw from foul territory/throw that pulls her off the white bag onto the orange bag). Would the runner be called for interference if she ran into the first baseman on the orange bag in those examples? Seems like a pretty dangerous situation to allow the fielder to use the orange bag under any circumstances -- the whole point is to avoid a collision at first.
Not if you coach your runners to use the bag not occupied by the fielder which in all but a DK3 situation should be the orange bag for the runner.
In a case where the fielder is on both bases I don't see where she would be protected from obstruction.