I do agree it's too easy to miss some of these, but you have a lot of misconceptions here. It's justified in-story why you can long rest as much as you want without turning, and almost everything you mentioned here is triggered externally, not by the number of times you have rested. Raphael can trigger on your first long rest if you progress far enough in the story first (I have had him show up on first rest, although I don't know what the exact trigger is). The companion interactions are triggered by your relationship level with them and/or your progress along their plotline. The parasite dream is triggered by overusing the tadpole in dialogue options.
That being said, you can't trigger all of these at once, so you still end up having to rest a dozen times to see them all, and it does seem like some dialogue is missable. I know on my first playthrough I was really hesitant to long rest until I got to the point where it was made clear the tadpole is being suppressed. They either need to make events stack (which would get kind of funky if you can build enough of them up at once) or forcibly have you long rest for certain story/quest milestones to keep the backlog down.
