The "glassy" clean sound of John Petrucci is the result of the splitted coils like you already mentioned.
It sounds so glassy becaus its the center coils, which means less bass from the neck and less treble
from the bridge. Can be heard on "Scarred" Track No 10 at around 5m12s on Awake.
The Amp was definitly the Triaxis, cause he used the Mark IIC+ only for dirty rhythm stuff.