Hello
In fact when you are using the build target "M5213EVB Internal ROM", the application is supposed to run from flash.
The vector table is then remapped to RAM and the content of the vector table is copied from 0x0000-0x3FF to 0x20000000-200003FF in the startup code.
This is done in module sysinit.c in function mcf5213_init.
This is done that way to allow you to update the vector table in the application itself easily.
So your S record file should contain the initial vector table setting at 0x0000.
Anyway S record file is supposed to contain only code and data located into flash. This is the file you have to use to program your flash.
I hope this helps.
CrasyCat