I used the lines on the mat exclusively for years, ad my poor mats are showing the wear, so I have started using the mat lines when I need to make a very long cut, or a cut something wider than my widest ruler, but otherwise use the ruler lines and cut across my mat at odd angles to avoid the "ruts". I haven't found any problems with cutting discrepancies so far, but my current project is very forgiving so problems may show up in future, more precise, piecing that aren't an issue now.
Alison