You cant change the tuning system on a guitar, (without adjusting the frets as someone else said) but adjusting the truss rod intonates the guitar to however you tune it. For instance, I play my 5-string bass tuned ADADG instead of the "normal" BEADG, and had to have the rod adjusted so that the notes would sound right the higher up the neck I play. The neck is meant to have a certain tension to keep the intonation, and once you mess with that you have to adjust it.