<p>Please just ignore the Boston Magazine piece. It is sloppy and inaccurate, as it attempts to do the impossible.
Commuting - rush hour (and you will be driving to school during rush hour and often back during it as well) is pretty bad in many areas. Just getting across Cambridge can take a while. Cambridge/Andover would be very slow (and as noted, you cannot be a day student from Cambridge) Cambridge/Milton will be time-consuming as well.
Milton is not really so much of a k-12 school as a k-8 and a 9-12 that happen to be together. A lot of kids come in at 9th so I think fitting in then is not a problem.
BB&N increases size a good bit at 9th and does a lot to help kids fit in.
As for cultural differences - look at the webpages and visit the schools. Nobody here will be able to give you a very strong sense of the personalities of the schools in a short posting.
Do consider that you should move into a town that has good public schools. Admissions to private day schools is very tough. (Public schools here are town-based, not county or state.)
And again, it all depends on what you want. There is no “Best school”.</p>