Hi,
lots of my birds spend time alone, doing their own thing. some go off and sleep in nest boxes some wander off to spend an hour or so alone excavating the muck heap. They do this regardless of their rank so I wouldnt see choosing to sleep in the nest box as a conciquence of being bullied. Also, as all the birds will be docile at night, this is actually when a subjugated bird would slink in last, tollerate a couple of pecks and quietly snuggle up to the others when they are too dosy to notice. I think she sleeps in the nest box because she wants to.
In terms of the pecking order this changes as birds grow and age and enviromental factors differ. In the warm weather when every one is out ranging, getting lots of excercise, pleanty of food and their attention is taken with hunting for bugs this usually reduces greatly. If it dosent my advice would be,
Be prepaired to remove a hen which is overly agressive and excessive in its treatment of the others as this can result in stress which can effect egg production, damage or death to other birds, nutrirional defficiency and illness in birds experiencing stress and lack of sufficient food.
Make sure the birds have lots of space and places to escape such as plants that they can hide behind but make sure they cant get trapped or cornered.
Put smaller or more docile breeds such as little pekins together in a separate coop
and make sure that you have lots of feed and water stations that are set far enough appart to pervent one bird guarding them all,
Buffy