追加の情報です。
AppStoreからダウンロードしたXcode6.2で正常な結果が返ってこなかったのですが、
試しにAppleDeveloperから同じバージョンのXcode6.2をダウンロードして確認したところ、こちらは正常な結果が返ってきました。
$ spctl --assess --verbose /Applications/Xcode-6.2_dev.app/
/Applications/Xcode-6.2_dev.app/: accepted
source=Apple System
両者をdiffで比較したところ、いくつか違いがありました。
以下、比較した結果です。
（Xcode-6.2.app がAppStoreからダウンロードしたもの、Xcode-6.2_dev.appがAppleDeveloperからダウンロードしたものです）
$ cd /Applications/
$ diff -q -r Xcode-6.2.app/ Xcode-6.2_dev.app/
diff: Xcode-6.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/Ruby.framework/Headers/ruby/ruby: recursive directory loop
diff: Xcode-6.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/Ruby.framework/Versions/2.0/Headers/ruby/ruby: recursive directory loop
diff: Xcode-6.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks/Ruby.framework/Versions/Current/Headers/ruby/ruby: recursive directory loop
Only in Xcode-6.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/share/man: whatis
diff: Xcode-6.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/System/Library/Frameworks/Ruby.framework/Headers/ruby/ruby: recursive directory loop
diff: Xcode-6.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/System/Library/Frameworks/Ruby.framework/Versions/2.0/Headers/ruby/ruby: recursive directory loop
diff: Xcode-6.2.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.9.sdk/System/Library/Frameworks/Ruby.framework/Versions/Current/Headers/ruby/ruby: recursive directory loop
Files Xcode-6.2.app/Contents/Developer/Platforms/iPhoneSimulator.platform/Developer/SDKs/iPhoneSimulator.sdk/System/Library/PrivateFrameworks/IMTransferServices.framework/IMTransferServices and Xcode-6.2_dev.app/Contents/Developer/Platforms/iPhoneSimulator.platform/Developer/SDKs/iPhoneSimulator.sdk/System/Library/PrivateFrameworks/IMTransferServices.framework/IMTransferServices differ
Files Xcode-6.2.app/Contents/Developer/Platforms/iPhoneSimulator.platform/Developer/SDKs/iPhoneSimulator.sdk/System/Library/PrivateFrameworks/IMTransferServices.framework/_CodeSignature/CodeResources and Xcode-6.2_dev.app/Contents/Developer/Platforms/iPhoneSimulator.platform/Developer/SDKs/iPhoneSimulator.sdk/System/Library/PrivateFrameworks/IMTransferServices.framework/_CodeSignature/CodeResources differ
Files Xcode-6.2.app/Contents/Developer/Platforms/iPhoneSimulator.platform/Developer/SDKs/iPhoneSimulator8.2.sdk/System/Library/PrivateFrameworks/IMTransferServices.framework/IMTransferServices and Xcode-6.2_dev.app/Contents/Developer/Platforms/iPhoneSimulator.platform/Developer/SDKs/iPhoneSimulator8.2.sdk/System/Library/PrivateFrameworks/IMTransferServices.framework/IMTransferServices differ
Files Xcode-6.2.app/Contents/Developer/Platforms/iPhoneSimulator.platform/Developer/SDKs/iPhoneSimulator8.2.sdk/System/Library/PrivateFrameworks/IMTransferServices.framework/_CodeSignature/CodeResources and Xcode-6.2_dev.app/Contents/Developer/Platforms/iPhoneSimulator.platform/Developer/SDKs/iPhoneSimulator8.2.sdk/System/Library/PrivateFrameworks/IMTransferServices.framework/_CodeSignature/CodeResources differ
Only in Xcode-6.2.app/Contents/Developer/Platforms/iPhoneSimulator.platform/Developer/usr/share/man: whatis
Files Xcode-6.2.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/6.0/lib/macho_embedded/libclang_rt.hard_pic.a and Xcode-6.2_dev.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/6.0/lib/macho_embedded/libclang_rt.hard_pic.a differ
Files Xcode-6.2.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/6.0/lib/macho_embedded/libclang_rt.hard_static.a and Xcode-6.2_dev.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/6.0/lib/macho_embedded/libclang_rt.hard_static.a differ
Files Xcode-6.2.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/6.0/lib/macho_embedded/libclang_rt.soft_pic.a and Xcode-6.2_dev.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/6.0/lib/macho_embedded/libclang_rt.soft_pic.a differ
Files Xcode-6.2.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/6.0/lib/macho_embedded/libclang_rt.soft_static.a and Xcode-6.2_dev.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib/clang/6.0/lib/macho_embedded/libclang_rt.soft_static.a differ
Only in Xcode-6.2.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/share/man: whatis
Only in Xcode-6.2.app/Contents/Developer/usr/share/man: whatis
Files Xcode-6.2.app/Contents/MacOS/Xcode and Xcode-6.2_dev.app/Contents/MacOS/Xcode differ
Files Xcode-6.2.app/Contents/_CodeSignature/CodeResources and Xcode-6.2_dev.app/Contents/_CodeSignature/CodeResources differ
Only in Xcode-6.2.app/Contents: _MASReceipt
それぞれ起動してXcodeビルド番号を確認したところ、どちらも"6C131e"でした。
なぜAppStoreからダウンロードした方はだめで、AppleDeveloperからダウンロードした方はOKなのでしょうか？
