Hello,
My wife and I started out exactly the same as you and your fiancé. She is and has always been straight. I was living as a lesbian at the time and not out to anyone about my trans status. She was separating from her (now ex) husband and I was getting out of a 6 year relationship. We met at work as well. We became close and fell in love.
This was a huge deal for her and was very confusing for her as well. She turned her life upside down with her family, her ex husband (since they have 3 children together), etc. All for me. About a year or two in, I told her that I had always felt like a man. She was very understanding and supportive. I used to say I wouldn't transition because it would be too hard for the kids and difficult for her family to accept. Plus work (we still work together).... But it became too much to bear. Like your fiancé, getting hormones and starting transition was very easy for me and luckily for me, I haven't lost a single person and work has been amazingly supportive. I started T 17 months ago.
We've been together for 8 years now and married for almost 3.
As for your main question - that's a tough one. My wife and I are very honest with each other and always have been, even when it's difficult. My lack of a fully functioning, natal penis is painful for us both. I know she feels... Cheated in a way. She never felt the way she does with me with anyone else. She finally found the love and connection she always wanted but we can't connect in that traditional male/female way. Trust me, I feel cheated too. So, yes, I would say that I think your feelings are very normal and not completely confined to being with a trans guy. Men assigned male at birth could have micropenis, no penis, or have had an accident rendering their penis useless... So I think these are normal and fair feelings to have.
However, that doesn't mean our sex life is unsatisfactory. There are a variety of different ways to get around that. The key for us is communication and being honest and vulnerable with each other. You may never "get over it". He probably won't. I know I can't. But we deal with it... And we do it together.