You didn't encounter such problems, just because ClangBase.lds already exists in your directory BaseTools/Scripts, as your building log below. But ClangBase.lds is absent in my BaseTools/Scripts, there is only GccBase.lds. Where did you get the ClangBase.lds?
GccBase.lds claims it is "Unified linker script for GCC and CLANG based builds", so I duplicate one and change the file name to ClangBase.lds. Now, building is successful, but I am not sure it is the right way.
We are use Ubuntu and GCC and we have notencounteredsuchproblems. Also You can check our topic about building universal payload. https://edk2.groups.io/g/devel/topic/universal_uefi_elf_payload/111543703