You get points or the work experience you claim. So if your do not want to claim points for a specific period where you worked, you can remove it from your work experience, and no work reference letter will be asked. There is no need to explain either.
Please be advised that you get maximum MEC points for 3 + years of work experience. You have to meet 67 points out of 100. So if you do, you can remove any work experience for which you do not wish to claim points.