I think that I have answered my own question - but this information may be of use to others so I mention it here..
The example bootloader created by the processor examples template makes a big assumption that the FIRST S Record downloaded to it is the HEADER (type S0 record),
which does not have any information that is needed or used to program flash. So, as
long as the this first record downloaded is always a header record and not a data record, it should be OK that the example bootloader code just throws it away. The Metrowerks tools appear to always create a header record in the output file, but for those who may use other tools, or who may have tools which post-process the output of the Metrowerks compiler should be aware of this.