it's often really hard to talk about how we feel and what we want, whoever and whatever we are withstanding...
It can be really hard for a man, trans or otherwise, to tell his partner, whoever they are, that they are experiencing sexual desires that are outside of their "normal" sexual interaction.
If you've always known him as a man, it can feel, to him, that admitting to you that he is curious about being penetrated is telling you that the sex life that you've thought was great maybe wasn't so, or that he's not really "all" man, or, or, or, or... whatever the reason he worries that it's going to ruin your relationship to admit that what he "wants" is different, for whatever reason, regardless of whether he's always wanted it and been afraid to admit it or not, it's something that he could legitimately be afraid to talk about.
I'm in a bit of a unique position as I'm someone who's actively involved in the whole bdsm subculture and blablabla and therefore I see posts on forums quite frequently that revolve around "how do I tell my spouse I want to X?"
It can often be something they've "always" wanted, and are starting to seek to actually do, but they feel, for whatever reason, that talking to their spouse about it would be just too much for them.
I also often see the "how do I get my spouse to X?" posts where the topic is about the person's "need" to fulfill a sexual desire with a spouse that has never expressed any interest what so ever in anything of the sort.
If what he wants is different enough from what the two of you "usually" do, then it can feel incredibly hard to say so.
I mean, sometimes it's even terribly hard to ask for something you "know" the other person is able to give because of one's own personal shame, which is most probably a factor here too. (If he cares about you, then he cares what you think of him. If he thinks that wanting to be penetrated is negative in any way, even just subconsciously, then he may very well fear that you'll think negatively of him. Depending on the level of internalized guilt over the desire, this fear may build to a level which is nearly impossible to overcome.)
I would not advise just being happy 'bout him running 'round with guys when you've agreed upon a monogamous relationship, but I would try to calmly talk to the boy, tell him that he can tell you what he wants, sexually and otherwise, even if it's something completely different than what you usually do, and while you may not be comfortable doing everything he wants that you won't think any less of him for it and that you'll do what you can to meet his needs without compromising your own so that you can both have a positive, enjoyable sexual experience together.
And, I'd suggest having the option to do this conversation in written form. That if he's afraid of your reaction that he should write down his wants/needs whatever and hand them to you that way, be it on paper or via email or whatever. It can be a lot easier.
There's a lot of trust lost, and I understand that, and I know it'll take a long time for him to rebuild it with you, if he wants to, but to do so would require communication, when you're ready of course, and for that the above may be helpful.
He does owe you mountains of apologies to say the very least. :/