In these fanfictions, a frequently seen theme is the clash of ideologies. Naruto, with his belief in friendship and peace, and Female Madara, who may have different views due to her background. Their relationship then becomes a way to reconcile these differences. Another theme is growth. Both characters grow as individuals because of their relationship. Also, the theme of acceptance is there. They accept each other's flaws and strengths, which is crucial for their relationship to develop.
Well, the theme of transformation is common. Female Madara may transform from a more cold - hearted or conflict - driven character to a more loving and peaceful one because of Naruto. The idea of destiny also plays a role. Some fanfictions suggest that they are meant to be together despite all odds. And the theme of discovery is there too. They discover new sides of themselves and each other as their relationship progresses.