The other day I was working on my guitar (Line 6 Variax JTV-89) that had some intonation issues. I noticed that I couldn't move the saddles in a position that would be satisfying (I was at the minimum position available on some saddles), but as the bridge can be moved, I used the screws to move the "high e" side a bit closer to the pickup.
So now my bridge is not parallel to the frets but has a slight angle (not much). Will this be a problem ? Can anything be damaged (neck, bridge, ...) ?
Here's an example of what a JTV-89 bridge looks like (this is not a JTV-89 but the bridge is the same). There are small horizontal screws that you can see on the left and right, near the vertical bridge height screws. So mine is slightly angled, the right part being closer to the pickup that the left part.