Except that you'd get somewhat skewed results since slowing down and then being up to speed by the next transponder has to have an effect on the total lap time regardless of where you begin timing.
Not really. You need to bear in mind that there are lots of transponders (not just three to cover each sector). There are transponders at the start and other points of each corner in many circuits. Also remember that you can move your "start" point for each lap. I.E. I can make transponder 15 (T15) my start point for lap 1, T17 for lap 2, T18 for lap 3, T15 for lap 4. In this case the driver can back of for 1 T, then pick it up again and hit another flying lap. In the above scenario only one sector on Lap 4 would be meaningless for the team, yet no other team would know your true lap times.
Having explained all that I just can't bring myself to believe any team would go to that much trouble to hide a lap time when there are so many other variables they can easily play with and, in the end, no other teams knows your variables anyway. I'm not convinced there's value in this.