You can change the Timecode of an MPEG before you encode in Compressor, in the QT MPEG Encoder, and even when background encoding within SP2.
If you're using Compressor, you will need to modify your preset. Go to the Encoder tab at the bottom of the Presets window, and look at the bottom of the Video Format section. There is a checkbox to Choose Start Timecode. Check it, then set the timecode.
I recommend making a Duplicate of the preset before modifying it.
There are similar settings in the QT MPEG Encoder and the DVDSP2 Encoding Preferences.
Hope this helps,
Jeff