We always have a small project called 'lineup' that outputs SD bars and 4 channels of audio (FCP) and just stripe up to where the ID board begins and then output our main program using assemble edit with timecode set to jam sync. Never had a problem.
And we use the same technique with our HDCAM decks; HD 'lineup' then assemble edit main program.
The concept of prestriping your tapes is doubling your head usage on the machine (as well as tieing it up for that length of time!).
Until recently we were using Velocity to edit, and it pretty much refused to assemble edit anything without timecode already laid on. In fact towards the end of the machine's life it was refusing to do a lot of things...
Some years ago as an edit assistant I was told it was good practice to black all DigiBetas before any editing use. I've believed that for years since. Maybe they were just trying to keep me busy?! And since then one of the tasks I've given *my* assistant has been pre-striping DigiBetas!