You misunderstand. You're not missing content because of your choices. You're just taking different paths with different scenes available to them. It will be completely impossible to encounter all the scenes in one playthrough. The game is designed around this philosophy. The concept of choice (that means something) is core and center to the design of Long Live the Princess. I don't punish "wrong" choices but instead, allow them to open new paths with different rewards. This will be even more true as I start to flesh things out after NG+.I love this game, but I also find it incredibly frustrating the more I look into it... It constantly seems to punish you and hide content from you based on your decisions. I put so much effort into proving Primroses innocence on time.. I thought I did the right thing that would allow me to see all the content, but what do I find when skimming the walkthrough? By doing that I am denied an entire section where Prim is in a cell and I can get her to be naked in there and have fun visits with her. So the game actively punishes me for playing well...
..and then I see there's all sorts of confusing decisions about rejecting/accepting advances (with no indications of which content I will arbitrarily be blocked from for choosing one or another) and well as choosing if girls are girlfriends or just friends without knowing if that means I'm being blocked from content with other characters as a result. What should be a fun experience of opening new content is becoming more and more a struggle against the games attempts to permanently block me from it's content. It's infuriating.
Embrace your choices. You'll have plenty of chances in NG+ to try different ones, and I will do my damndest to make sure it's fun and not tedious to go through the game in that mode.