The standard binary file format generated by the linker for the Apple ][ target is a binary program with a 4 byte DOS 3.3 header containing the load address and load length. The default load address is $803.
AppleCommander 1.3.5 or later (available at
http://applecommander.sourceforge.net/) includes the option
that allows to put binary files with a DOS 3.3 header onto disk images
containing DOS 3.3 as well as ProDOS 8.
For ProDOS 8 system programs the load address is fixed to $2000 so there
is no need for a header. Thus the linker configuration
apple2-system.cfg for those programs
omits the DOS 3.3 header. The right AppleCommander option to put system files
without a header on a ProDOS 8 disk image is