This is a very good question indeed, as I have also noticed that the MainConcept encoder in Encore & Premiere seems to do this.
I did a double-check by installing a trial version of Vegas - this also uses the MainConcept encoder - and in an NTSC project, it will automatically set colour profiling options and I suspect that this will include resetting the luminance from 0-255 to 16-235.
In vegas you can get around this by turning off the colour profiling.

When I use Encore, I admit I simply only ever feed it compliant M2V files. The obvious workaround to try here is to feed it with an AVI or a MOV file without the luminance correction, and see what that looks like. Perhaps not ideal, but worth a try as an experiment?