To reproduce:
1) Open attached project
2) In top menu, select 'Portfolio -> Asset Bundles -> Build Asset Bundles' and 'Portfolio -> Build Viewer (Release)'
3) Copy web.config xml from <ProjectFolder>/Servers/AssetBundlesServer to ViewerServer
4) In ViewerServer folder, edit the .json to the path of where you will be linking your asset bundle server
5) Use IIS to make two servers, one pointing to <ProjectFolder>/Servers/ViewerServer, another pointing to <ProjectFolder>/Servers/AssetBundlesServer
6) Open ViewerServer website
7) When it loads, press U
8) If Url is unchanged, change it to point to AssetBundlesServer (even though textfield's cursor is invisible, you can move it and delete only main name)
9) Click Red Paint in menu

Expected: Because user is forcing non-stripping of Substances with link.xml, nothing wrong happens
Actual: Error pops out in console that the code was stripped out

Reproduced in 5.5.0p1, 5.6.0f2, 2017.1.0a5