To reproduce:
1) Open the project and "thing" scene.
2) Select Edit->Project Setting->Graphics, set Instancing Variants to Strip Unused.
3) Check "Alt-Color.shader" and shader variant collection at "Asset/AsbThings/BundleA/All". There are three variants in it and include "INSTANCING_ON".
4) Open "assetbundle browser" on Window->AssetBundle Browser, mark "Force Rebuild" in it (if you want to see the expected result
5) Build the bundles
6) Run the scene.
7) Click the "load" button in the game view.

Actual: The cube will display as blue color (it means INSTANCING_ON has been stripped)

8) In Graphics settings, set Instancing Variants to Keep All
9) Repeat steps 4-7

Expected: The cube is red now.

Reproduced in 2017.1.0p5, 2017.3.0f3, 2018.1.0b1