The boot cloner doesn't read the bootstrap from the device. It has the bootstrap code compiled into the sketch. You can stick in any bootstrap code you like with a handy program to format it into C source.
I didn't find anything in the boot cloner to do it, but this little bit of code will take a .hex file and format it nicely for inclusion in the bootcloner sketch.
#include <stdio.h>
#include <string.h>
main()
{
char buf[4096];
int n = 0;
while( fgets(buf, sizeof(buf)-1, stdin)) {
int len = strlen(buf);
char *b;
if ( len < 9) continue;
buf[len-4] = 0;
for ( b = buf+9; *b != 0; b += 2) {
printf("0x%c%c, ", b[0], b[1]);
n++;
}
printf("\n");
}
printf("/* %d bytes */\n", n);
}