Reproduction steps:
1. Open user's attached project ("TestEmissionBug")
2. Enter the playmode and click on the cube
3. Inspect change of cube's shader
4. Build and run the game
5. Click on the cube, inspect that shader did not change

Expected: Shader settings change both in Editor and in the Built Game
Actual: Shader settings do change in Editor, but do not change in the Built Game

Reproduced in: 2017.2.3p2, 2017.4.7f1, 2018.1.9f1, 2018.2.1f1, 2018.3.0a6

Update:
Unused shader settings are excluded from the build and can not be modified in the Built Game.

Workaround: Creating second material with enabled settings and switching to it in Built Game.