If you let society and yourself repress your emotions and wishes, you'll never live freely and you'll regret it later.
Better to make a mistake than not to do anything.
It's not that she fears he won't have sex with her.
It's that he never showed her this kind of friendship and easy companionship. It hurts her because she wishes she could have it and she feels like it's out of her grasp. She should know though that it will come with time.
A threesome could totally work! Tsubomi is not on the same vibe as what Ueno and Moka feel for each other. She wants to be friend, and she wants to share everything with them including sexual experiences. But I don't see her trying to steal anyone.
Let her in! Welcome her! She brings fun...
You can't recommend this manga because the world is full of people who will shame us for normal things. It's like living in prison where all of your acquaintances are your jailers.