I'm not sure what you mean about "copying the output of xcodebuild". What I've done in the past is save one output to "x86_64/myproj.framework" and the other architecture to "arm64/myproj.framework". Save yet another version to just "myproj.framework". Take any "executables" (tools or dylibs) from the two architecture-specific versions, lipo together, and write into the appropriate place in the universal version. Then sign the universal version.