I'm actually surprised that a thread like this exists on this site, since it is rare enough to find somebody even willing to talk about and analyze this fetish, let alone have it in the first place.
I wanted to offer my input since I have the same fetish, except in my case (since I'm a woman) it's called cuckqueening. I'm lead to believe it is rarer for a woman to have this fetish. Over the past two years I've explored why I have developed it and I've come to several different conclusions. In regards to the OP:
This seems to ring true for me also, although my father wasn't absent in my childhood years, he did disappear for the majority of my teen years from age 14 and up. We have a complicated relationship and while there is a physical distance (he lives in Texas and I in the UK, it has been this way for several years as he now lives with his new wife), we also have many personal differences and points of view that have caused problems between us, trying to navigate a way to form a friendship with him consolidating all of this together has proved difficult but not impossible and we talk often. However, our situations don't seem to be that rare, and I have spoken to a few people online with this fetish who did not have an estranged parent at all, or any kind of abusive background.
Agree with Mishelle that sexuality is incredibly complex and a fetish, in my opinion, can't be traced back to one singular event, but a series of events that interact with each other over time. I do however believe that my father and his absent role in my life might have something to do with it. For me, it's always the man I am with who has sex with other women in my fantasy, however the Alpha male types do stand out above the rest. I have one particular ex who meets the Alpha male criteria and he features heavily in my fantasies. Perhaps this is our way of dealing with the male figure in our lives who let us down? It seems to be that way, when I read your OP. But then explain those who don't share this in common?
I will say however that your last post seems concerning to me. If you recognize that this is a fetish and try to eliminate it altogether, you'll encounter problems. Fetishes don't just 'go away'. They are, for the most part, here to stay, unless you decide to take the route of therapy, and even then there is no guarantee that it will be removed from your psyche entirely. Mostly I am concerned as to why you want to rid yourself of your fetish. Does it harm you? Do your partner's negative feelings toward it have anything to do with your decision to ignore it? Really, this fetish doesn't harm anyone. It is at it's core a form of humiliation, and humiliation is a common theme in sexual fetishes and kinks. But I also want to add in exploring my fetish and why it has come to be, I've come to a level of acceptance. I figure that if I enjoy it, if I can have it while not relying on it entirely for sexual gratification, and if whomever I am with can tolerate it, then that is all I need. Dependency levels will vary from person to person but to be perfectly honest, if you can enjoy sex with your partner without it at least some of the time, why ignore that part of yourself?
I've taken my cuckqueen fetish to a point where I accept that I am polyamorous and would be happier in an open relationship, and have expressed this to the men and women in my life. Some are uncomfortable with the idea and I'm still working out the kinks in these relationships, but overall I am happy with where I am at and I am still able to enjoy indulging in other fantasies and fetishes of those whom I am with. Is this at all possible for you? Perhaps instead of over-analyzing your fetish, it's better to accept that it is just a part of who you are, and approach it that way.
*EDIT* Also, forgot to address this quote in particular: "She told me that she would prefer if I didn't have the fetish because she isn't a fan of how there are a lot of emasculating aspects to it. She said she would prefer that I stick to roleplay/fantasy talk in ways that make her feel submissive to "her man"...". She seems to hold a traditional view of sex that she has perhaps hidden from you for fear of you leaving her. It sounds like she'd rather you not have this fetish at all and be dominant the majority of the time. Sorry, but I disagree with that entirely. You can't be someone that you are not. If she can't accept that this is who you are, then well, what can I say. I have left people for this very reason.