The question basically boils down to whether it is allowed for a female aspirant to perform the Yogic postures or not. And, the answer is yes, but I don't have any direct reference.
Yogi is the term used to denote a male aspirant who is adept in the practice of Yoga. For the women the corresponding term exists in scripture and it is Yogini.
Hatha Yoga Pradipika (in the 3rd chapter) itself uses the term Yogini on more than one occasion.
Rakshedākuñchanādūrdhvam yā rajah sā hi yoghinī
vetti khecharī cha bhaveddhruvam |
She who preserves by upward contraction her rajas is a Yogini. She
knows the past and the future and certainly attains perfection in
So, it is here implicitly implied that a female aspirant can also perform all the practice mentioned in the text and hence she can also practice Siddhasana which is one of the many Yogic postures defined in the text. As for the mention of the male organ in the verse, IMO it should be understood as an indication of the place where the heel is to be placed and not as indicative of something else.