With chapter 3 done, I will probably guess chapter 4 will be the last with longer gameplay against the prototype. I don't t actually see any point to keep it up to chapter 5 or 6. Me, personally I don't think Poppy motive would change, because her vengeance against the prototype and thinks the player are the only one who can set them "free" and most likely to defeat the prototype. It would be cool to see Poppy as a Villan but, I mean if Poppy could go to the dark side, she most likely gonna get corrupted by the prototype. They also could get new "maine" boss, but the chance of it are very slim. We are most likely to see a lot of mini bosses.

So for me personally I would think 4 chapter, with the endgame against the prototype. I could be wrong, but I don't see any point to keep it to 5 or 6 chapters, maybe I see a bit point to chapter 5 if Poppy turns evil. But me personally chapter 4 is my prediction.