My advice is to just keep telling him that you won’t miss cismen and their parts. Most transmen prefer for male descriptors to be used to described to their bodies—recognizing that you see him as male may help alleviate that stress.
I can’t say that it will ever go away. It might when he feels comfortable in his body and with your relationship, but it may always be present. My boyfriend likens this feeling to the feeling some women have about their weight. Some women will always have a fear that their men will leave them for someone skinnier no matter how many times her partner says she’s beautiful. Others feel more secure as the relationship progresses.
I wish the two of you the best of luck. These issues can be serious, but I think the both of you can work together to make it better.