Your question was a very good one and this is all very good advice. However, the same problem occurs with the ruler. The lines on rulers are larger than the rotary cutter. Do you use the center of the line, the right side or the left?
The key is still consistency. You need to pick one and stay with it. Because not all rulers are the same, I do a test piece and measure after cutting. For example, if I want a 3 inch strip, I cut a test strip using the center of the line. I measure it to be sure it is 3 inches. If not, I move to the left or right accordingly. I use those colored tapes to mark the spot I need and stay with that mark for my project.
This takes more time, but saves me time in tearing out mistakes due to bad cuts. Good luck.