No, no... you don't switch major scale boxes, that's not it. If you play G-C-D as your chords progression, you can play an E Aeolian Box, an A Dorian Box, D Mixolydian Box, or whatever, but it's still G Ionian. You see, it's all about the tonal centers. G is the tonal center of the progression. The idea is to play G modes, like G Ionian, G Lydian, or G Mixolydian over the progression. Playing A Dorian is the same as playing G Ionian.

However, if you have a tonal center of D in a progression of Dsus2-D, Cadd9-G, the tonal center is D, even though the progression show that the key is G Major. In this case, you would use D Mixolydian, D Ionian, or D Lydian. You want to use modes based off the tonal center of the progression, not modes of one single major scale (because as you said, they would all sound the same). Using G Ionian, A Dorian, etc. over this progression would sound just like G Ionian the whole way through.