Reproduction steps:

1. Open "Tests_UnityProj.zip"
2. "Test" -> "BuildPipelineTest" *
3. See that outside the project folder a Build folder was created
4. Exit the Editor
5. Right click on Editor launcher -> "Properties" -> "Target", add " -batchmode -quit -TestBuild" -> "Apply"
6. Launch the Editor
7. The Build failed, See Editor.log ("Ctrl" + "F" -> "Assets/Plugins/Test.cs")

Expected Result: The Build finishes in Batch Mode
Actual Result: The Build fails with a 'missing assembly reference' error

Reproduced with: 2017.3.0a3, 2017.3.0a1, 2017.1.0a2, 2017.1.0a1, 5.6.3f1, 5.5.4p2, 5.5.3p4, 5.5.2p4, 5.5.1f1, 5.5.0f3, 5.5.0a6
Regression introduced in: 5.5.0a6
Did not reproduce on: 2017.2.0b6, 2017.2.0a1, 2017.1.0p3, 2017.1.0f3, 2017.1.0b1 and 2017.1.0a4 and 2017.1.0a3(Doesn't build, but no errors appear), 5.4.6f1(Custom Editor functions don't seem to work)

Note:
* If your Target Platform is different, for e.g. Windows, then open "Editor" -> "TestBuilder" and change line 24 from "buildOptions.target = BuildTarget.StandaloneOSXIntel;" to, for e.g., "buildOptions.target = BuildTarget.StandaloneWindows64;"

Instead of adding " -batchmode -quit -TestBuild" ,add " -batchmode -quit -executeMethod TestBuilder.BuildPipelineTest", it fixes the issue

Error:
error CS0234: The type or namespace name `UI'** does not exist in the namespace `UnityEngine'. Are you missing an assembly reference?

** Or "EventSystems" or "Text"