The standard binary output format generated by the linker for the Atari target is a machine language program with a standard executable header (FF FF <start address> <end address>). These values are calculated in the crt0.s file from the __CODE_LOAD__ and __BSS_LOAD__ values, so keep this in mind if you create a custom linker config file and start moving segments around. You can override this behaviour by creating your own crt0.s file and linking it into your program. A run vector is added to the end of the file ($02E0 <run vector>) and is calculated using __CODE_LOAD__ in crt0.s also.