You got it.
In my opinion, the second is preferred even though yes, it must evolve the start ahead of any reproduction logic. My reason is that starting from pure 0's imparts the least information and therefor maximizes flexability in how evolution may proceed. One may argue that the start does not add much information, but it adds something. It gets placed at the beginning for one thing, where evolution probabily would evolve junk DNA ahead of it which could possibly come into play later.
That said, it's a minor nuance to be sure. In particular, entires whose ancestrial genome contain a start are elligable for the conditional logic evolution prize.