Even before you run Autohide routine, you need:
1. In Modify > Cloth Layer Settings" make sure the inner garment is assigned lower layer number than the outer. Example: Bra - 1, Shirt - 3 Jeans - 4 (if shirt is tucked), Jacket - 5
2. Execute "Run Collision"
Only after that try Autohide. Thought it does not always work well. I prefer to hide faces manually in Edit Mesh, where I feel it is necessary..