This is why I was happy to see Christopher Schlegel's approach to the pentatonic scale here in GT. Yes, thinking about boxes makes it easier to remember but it shouldn't make you static in your playing. Once you've learn the boxes, you need to learn how to link them and I think this is where most books fail.
Then again, if you would show all the notes of a scale on the entire fretboard..... that would make it very hard to memorize them. So I beleive the key lies in making memorizing entire fretboard scale by breaking them into smaller pieces "but you need to teach how to link the peice" lol Otherwise it's very hard for the student to learn how to effectively use link those small parts.