Reproduction Steps:
1. Create new project
2. Build to iOS
3. Run terminal
4. Navigate terminal to Xcode project location (cd <path)
5. Run "xcodebuild" terminal command
6. Notice warning being thrown:
[MT] PluginLoading: Required plug-in compatibility UUID DFFB3951-EB0A-4C09-9DAC-5F2D28CC839C for plug-in at path '~/Library/Application Support/Developer/Shared/Xcode/Plug-ins/Unity4XC.xcplugin' not present in DVTPlugInCompatibilityUUIDs

7. Delete symlink at this directory:
/Users/<username>/Library/Application Support/Developer/Shared/Xcode/Plug-ins/Unity4XC.xcplugin

8. Run "xcodebuild" terminal command again
9. Notice that warning is no longer thrown

Expected behaviour: Unity cleans unnecessary files that interrupt correct behaviour.
Actual result: There is symlink file that causes "xcodebuild" terminal command to throw warnings.

Reproduced on versions: Unity 5.4.1f1, 5.4.5p3, 5.6.1p4, 2017.0b9
Reproduced on Xcode versions: Xcode 7.3.1, Xcode 8.3

RESOLUTION: WONTFIX, because the issue is very minor and fixing it would require to remove Build&Run support for Xcode 7 and earlier.