Reproduction steps:
1. Open project attached.(Repro.zip)
2. Open scene "SimpleSample".
3. Press Play.
4. Detect that there is error "UnityEditor.BuildTarget.WebPlayer is obsolete..." and due to this remove 27-34 lines from Settings.cs.
5. Save and go back to Editor.
6. Try to start.

Expected result: You will be able to enter play mode.
Actual result: For some reasons error appears: "An assembly with the same name `UnityEngine.UI' has already been imported."

Notes: After restarting Editor error goes away.

Reproduced on: 2017.3.0a1, 2017.3.0a6.
Works fine on: 2017.1.0p5, 2017.2.0b9.
Regression introduced in 2017.3.0a1.