I mean more that those options will prevent you from obtaining the true ending in a single playthrough, regardless of your Nagisa score up until that point. You will need to run the chapters again picking the right options.
4-2 is a bit of a messy area that I'm not too clear on entirely due to the whole fighting a main storyline NPC thing. But basically make the right choice and you can't go wrong regarding the true ending.
For a simpler way to manipulate your ending - assuming you follow the already posted guide for true end - you can..
Bad End: Bad choice in chapter 4-2
Normal End: Pick the lower option after 5-1 boss (if no dialogue options shows, you are already on track to receive it)
True End: None of the above, with correct story choices (which generally follow the pattern of 'believe/talk/defend/feed/agree with Nagisa' at most opportunities)
It is impossible to permanently lock your character in to any given ending so don't sweat it, you may just have to run missions again to undo your naughtiness or raise your Nagisa score. It is completely possible to run all the story missions multiple times on the same character to get all rewards/titles.
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