Steps to reproduce:
1. Open User's attached project
2. Open scene "Main"
3. Press Play. Notice: object is moving, a magenta line is seen, in Console: m_NavMeshAgent.isOnNavMesh:True
4. Build the project
5. Open build

Result: Object is not moving, a magenta line is not seen. NavMeshAgent is not created. Player Log file outputs: m_NavMeshAgent.isOnNavMesh:False

Reproduced with: 5.6.0b5, 5.5.1f1, 5.4.4p3, 5.3.7p2.

Note: reproduced with Windows, macOS, iOS.

Workaround:
1. Create an Empty Object in your scene
2. Add a Nav Mesh Agent component to that Object
3. Build AssetBundle

By Design:
The issue is that code stripping does not know about the nav mesh in the asset bundle, so it gets stripped out in the build. Use BuildPlayerOptions struct (https://docs.unity3d.com/ScriptReference/BuildPlayerOptions.html) and set the assetBundleManifestPath property to the main asset bundle manifest file generated when asset bundles were built.