Altering only the tension, or thickness, or length of a guitar string is bound to alter its relationship to the fixed frets beneath it, and will consequently change the intonation, however slightly. Another factor is the action, which will be slightly lower with slackened strings, so any built-in compensation (at the bridge) for the fact that the string has to be pushed down to the fret and made tighter/sharper will then be inaccurate. If you want to tune the whole guitar down, use heavier strings so that the overall tension on the neck is more like it should be and the action is roughly the same. In other words, if you alter one parameter (tension), then some compensation has to be made elsewhere (thickness and/or length) for the intonation to remain constant. The only sure way is to let the maker set up the instrument according to how you are going to use it. Sad but true; I am also a victim btw.