Tsubomi still doesn’t feel right doing it with him. She also doesn’t like how they’re inexperienced, while Yuuto been having it with other girls. And, they both said they’d rather have their first time with each other. 

Liking the author’s choice in this. Tsubomi and Lien had been having nice chemistry with each other in the story. So keeping them like this rather than forcefully making them suddenly become in love and infatuated to Yuuto feels a lot more consistent (and provides a variety). Don’t have to take everyone into the harem.