I'm not sure that Dare returned to present day, I think she may have stayed in the past with Aten.
As for Marethyu letting her kill her Elder, I think that may have been more because he needed Dare to be free rather than who her Elder was. It may have been convenient that her Elder was an enemy, but I think it was more important to have Dare as a free agent so she could carry out her task on Danu Talis. Had she still be tied to her Elder she may have never helped Dee and gone back to Danu Talis in the first place
And I agree I don't think her Elder directly gave her the flute, the passage that talks about her going to find it does not imply her Elder was present. I think if her Elder had been they would have tried to secure the flute for themselves or at the very least kept her from it. I'm also wondering if she found the flute after she killed her master.