Reproduction Steps:
1. Open User's project
2. Delete all AssetBundles in "StreamingAssets/GeneratedBundles"
3. Make Sure that "Always Included Shaders" list does not contain "Legacy Shader/Diffuse"
4. Build AssetBundles "AssetBundles/Build bundles"
5. Open "AssetBundles/Open Viewer"
6. Select "treamingAssets/GeneratedBundles/textured_cube"
7. Double Click on "Legacy Shader/Diffuse"
8. Notice that it is Precompiled
9. Add "Legacy Shader/Diffuse" to the "Always Included Shaders" list
10. Build Again
11. Notice that "Legacy Shader/Diffuse" is still precompiled

12. Delete all AssetBundles in "StreamingAssets/GeneratedBundles"
13. Build again
14. Notice that "Legacy Shader/Diffuse" is only referenced

Expected behaviour: AssetBundles are rebuilt when "Always Included Shaders" list is changed.
Actual result: AssetBundles shaders are still precompiled after "Always Included Shaders" list is changed.

Reproduced on versions: Unity 5.5.3p2, 5.6.0f3, 5.6.0p3
AssetBundleViewer Does not work on Unity 2017