Who has custody when stepchild is put under stepmother's protective order against father?

An order of protection does not give custody per se, it gives possession. If step-mom wants custody, she need to seek leave to intervene in the divorce or parentage case and ask that court for custody. She could also seek guardianship of the child.

At this point step mom and probably mom, if she is around and there is no custody order. If no mom, step mom should petition to be named the guardian of stepdaughter.

We may not have all the facts to properly answer, but if you are saying that the court in fact granted her the protective order with the inclusion of the child (so not just that she is filing for that in the hopes of getting it), then the order should spell out that she has temporary custody. But there needs to be strong evidence of violence or threat of violence to the child before DV judges typically entertain even temporary custody in a DV order. Either way, it will always be superseded by any subsequent actual custody action in regular district/family court.