Got it! This part of the walkthrough -
"NOTE: If pursuing Trapper, do NOT resist and do NOT scream."
- applies to more than just Trapper's route. Even without pursuing Trapper, resisting and screaming locked me out of romance options.
(Also, I had the option to choose every route, even though I only flirted with Flowey?)
I'm hoping this either gets fixed or gets explained in an updated walkthrough lol