A 250 seat config doesn't quite make sense. The 787-9 is roughly the same length as an A330-300, which fits almost 300 pax at the moment. Even if a chunk of Y seats are taken out and are replaced with Y+, we would still be looking at around 270 while maintaining a 2-4-2 config in the back. So either they're going to fit a a quite a few more J seats in, or it's possibly going to be a 4-class bird, especially if they consider 3-3-3 in the back.
I'm indifferent for a 3-3-3 in the back, keeping in mind that in a 2-4-2 config, pax will start losing empty seats next to them from about half full and there are 4 middle seats in each row, while the same doesn't happen with 3-3-3 until more than 2/3 full, with only 3 middle seats in each row. Let's take a 80% load for example, (close to the 81.5% as stated in the presentation for QFi). Based on an evenly spread pax load, on 2-4-2, only 1 or 2 pax would have an empty seat next to them (depending on where exactly they sit), but on 3-3-3, at least 2 pax would have an empty seat next to them (unless some demented person decides to take the middle seat and leaving one empty seat for his/her own exclusive use). Quite a few rows would even have 4 pax who won't have anyone in the seat next to them.