I have found that the writing of FTM stories are greatly more challenging than their MTF counterparts. By this, I exclude body/mind swaps and stories that include both MTF and FTM at the same time. I mean exclusively a story that features two straight female friends and one of them ends up a straight male by the end of the story. I will try to sum up the difficulty in writing this kind of story and why they are so rare.
1. Low Demand: FTM are in low demand and by my estimate 99% of stories on any given website will feature some kind of MTF. This is highly discouraging for writers but there is an opportunity to create a rare gem if the story is written well. My goal is to create that gem.
2. Mechanism of Change: A common feature in magical stories is that a man's "seed" can be used as a mechanism to change another man into a woman. Additionally, the penetrative act of a man on another man can also cause the change. With two women, the mechanism of change is more challenging to write.
3. Submissiveness problem: It's generally the case that the one being transformed is the submissive one being forced or inviting the change from someone else. Since women are generally submissive this works out well for MTF stories. However, its more challenging to narrate a women turned man becoming submissive before another woman. Therefore, a woman turned man will need to be both dominant and undergo a change at the same time.
4. Author's Personal Experience: It's difficult for a male author to narrate the thoughts and feelings of a female protagonist undergoing change. MTF authors may find it unsettling to write and discuss the very idea of a FTM as that would be the very opposite of their life goal.
5. FTM Cross dressing: In this day in age, women can wear fairly masculine clothing and not be remotely TG. Essentially a suit would be required in order to dress ultra-masculine. Women tend to have more unique and expressive fashion whereas men tend to have a very uniform fashion. This leads to less creativity in detailing the fashion in the story than with a MTF. Also, there is considerably more taboo with a man wearing a dress than a woman wearing a suit. Detailing the use of make-up and hairstyle is also subdued in a FTM story than a MTF.
6. Less Risk: There is considerable more risk, taboo, and potential humiliation in a MTF than a FTM. In today's society, a tomboy or masculine girl may even be praised and accepted by her peers. The same cannot be said of a boy acting and dressing as a girl. Less risk means less drama and consequence to the protagonist.
7. Sexual Chemistry: To put it simply, a man may put aside the reality that a MTF was formerly male if she is sexually attractive. The same is not necessarily true of FTM whereby a woman may judge the former female for the following attributes: intelligence, humor, looks, strength, personality, wealth, connections, academic record, professional record, and the list goes on. Simply put, an ordinary woman isn't going to have sex with a man just on looks alone. Therefore, the FTM will have to work harder to achieve the same goal.
8. Homosexuality: A MTF story involving a Lesbian relationship is going to be more accepted than a FTM story involving a Gay male relationship.
9. Humiliation/Pain Stories: These stories are more likely to be accepted as MTF than FTM because the mental and physical torture of a woman to make her a man risks being seen as misogynist and sexist.
10. Age Gap: An age progressive story involving a girl becoming a man and then having a relationship with a girl is taboo and socially unacceptable to many people. However, an age progressive story involving an older woman and a younger man is not as taboo. Even while being younger, the young man may still be considered the more "dominant" of the two. An older man and a much younger woman is excessive dominance by the man.
I am sure there are other reasons but these are my top 10. Honestly, I would like to find more FTM stories that exclusively focus on two women/girlfriends. I completed Linking Spell: A Woman's Desire as an example and I am working on a large novel size FTM to be posted in the near future.