The SDK and os versions were hard coded.  Archs were mixed up.
Because of this,  Was getting errors with latest SDK:
clang: warning: no such sysroot directory: '/Applications/Xcode.app/Contents/Developer/Platforms/iPhoneOS.platform/Developer/SDKs/iPhoneOS9.2.sdk/' [-Wmissing-sysroot]
clang: warning: no such sysroot directory: '/Applications/Xcode.app/Contents/Developer/Platforms/iPhoneOS.platform/Developer/SDKs/iPhoneOS9.2.sdk/' [-Wmissing-sysroot]
clang: warning: no such sysroot directory: '/Applications/Xcode.app/Contents/Developer/Platforms/iPhoneOS.platform/Developer/SDKs/iPhoneOS9.2.sdk/' [-Wmissing-sysroot]
In file included from external/com_google_protobuf/src/google/protobuf/io/printer.cc:35:
In file included from external/com_google_protobuf/src/google/protobuf/io/printer.h:40:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/string:470:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/string_view:171:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/__string:56:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/algorithm:638:
In file included from /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/cstring:61:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/string.h:61:15: fatal error: 'string.h' file not found
              ^~~~~~~~~~
              1 error generated.

Currently none of these are needed when using bazel with https://github.com/bazelbuild/rules_apple.
-target arm64-apple-ios is passed properly to clang.  So -arch armv7 etc are not needed.
OS_IOS is not used anywhere.
Sources have:  GOOGLE_PROTOBUF_NO_THREADLOCAL defined in src/google/protobuf/stubs/platform_macros.h for iOS.  So __thread= is not needed.  In fact now that bazel is using C++11 by default,  __thread should ideally be moved to thread_local.
-miphoneos-version-min is passed by rules_apple.