The standard binary output format generated by the linker for the Apple ][ target is a machine language program with a 4 byte DOS 3.3 header. The standard load address is $800.
The DOS header is in its own segment named EXEHDR. If you don't want the
header for some reason, you can change
HEADER: start = $0000, size = $4, file = %O;
to
HEADER: start = $0000, size = $4, file = "";
in the linker configuration to have the linker remove it.
Please note that there is a "Apple ][ ProDOS 8 system program for loading binary programs" available in the cc65 User Contributions section. It adds all benefits of a ProDOS 8 system program to the standard binary program generated by the linker for the Apple ][ target.