The issue seems to happen when you create a model that has parts of it that are not connected to the main mesh, but are still considered as part of the mesh (for example, when a primitive is created while being in edit mode in Blender).

To reproduce:

1. Open the project, attached by the tester (multiMeshRendering.zip)
2. Open the "scene" scene
3. Select cubeFBX game object in the Hierarchy
4. In the Inspector, in the Material section change Rendering Mode to Transparent

Expected: changing Rendering Mode to Transparent on a standard shader doesn't make parts of the mesh to always render on top of other parts of the mesh

Reproduced in 5.6.0a1, 5.6.3p3, 2017.1.0f3, 2017.1.1p1, 2017.2.0b11, 2017.3.0a7
Did not reproduce in 5.5.4p2
Regression introduced in 5.6.0a1