I have also noticed once the same thing. I don't think turning off the phone and starting it again will take away 6% battery but rather I think the battery stats were probably wrong and showed 100% charge while the true measurement was around 94%.
I think it is done intentionally so that the battery doesn't degrade easily in future.
As said above leave the phone for charging for more than 30 min after 100%, you will see increase in battery life dunno how it affects the battery cycles in future.
Nexus 5- 32Gb D821
Nexus 7 2013-16Gb flo