The significance of female free will, or agency, in Shakespeare's Twelfth Night hinges on the fact that the women steer the plot line entirely. Maria, Olivia's servant, authors the practical joke against Malvolio which creates one of the most comical scenes in the play where Malvolio struts his stuff for Olivia's love with yellow socks and smile that won't quit. Without Maria's wit, the scheme would not have played out successfully nor created more contention between Malvolio, herself, Sir Toby and Sir Andrew.
Olivia's free will allows her to choose with whom she falls in love. Olivia refuses to bend to Duke Orsino's persistent wooing. Olivia decides to fall in love with Cesario and to marry Sebastian whether Orsino likes it or not. During a time when women usually did not have much of a choice on who they married, Olivia retains control of her choices even though she too is a bit fooled.
Viola, on the other hand, seems to loss control of who may fall in love for her when she choosese to disguise herself as a man in order to get work. Little did she plan on falling in love with her new employer! She does her best to woo Olivia in his stead, but ends up gaining Olivia's love. Viola, in a sense, actually loses a bit of her own agency after making a drastic choice. Still, all is rewarded to its rightful owner in the end of all of Shakespeare's comedies and she is no different.