Qbs passes "-m elf_i386" for x86 and "-m elf_x86_64" for x86_64. It sets System V ABI in the final ELF. While such binaries seems to work on FreeBSD, some tools report that they are not FreeBSD ELF objects. The correct flags are "-m elf_i386_fbsd" and "-m elf_x86_64_fbsd".
Workaround: set correct flags in a profile's cpp.targetLinkerFlags property.