I am not a Penguin rep, but I think I can safely say that yes, any gimmick or gaff that's included in the package will be included in the Flat Pack. All they exclude is superfluous packaging that adds weight and depth, like DVD cases for example.
I just received a Jay Sankey effect that included two gaffed coins, under the "Flat-Pack" banner. Both coins were included and the DVD was in a flat envelope, not the thicker DVD case.