I know which exchange you're talking about and it leads to one of my favorite lines in the game:
MC: Do.. do you want me to grab a condom?
Meredith: No, Sweetie. No condoms.
If we're going to break a taboo, we're going to do it in style.
MC: Oh.
MC: OH!!!
I've established an informal rule that the women in this game (unrealistically) react unfavorably to the suggestion of birth control and will let you creampie them to your heart's content without any expressed caution or concern over pregnancy (or STDs). If you don't want Pregnancy, it's incumbent upon you as the player to practice "safe sex" and turn Pregnancy off in the Options Menu.
Meredith is going straight to bareback the moment she decides vaginal penetration is on the table. Kinks range far and wide, but I have NEVER heard of anyone who is REALLY into condom sex. My best evidence to support this is that if I type "condom" into reddit, the top recommended subreddit is "condomremoval." Therefore, my view is that having condom sex is just going to be a scene designed to appeal to no one. If I want to tease the player, there are plenty of other ways to do that. I recommend the "outercourse" and "pussyjobs" subreddits for demonstrations.
That said, you've pointed out a continuity issue with that scene. I definitely don't want the Bonus scene to be their first time and there's
never going to be condom sex in this game. What I'll probably do to solve this is move the "break a taboo in style" exchange to the first time they have sex and take it out of the bonus scene.
P.S. Thank you for pointing this out. I wouldn't have noticed otherwise. Cheers!