After recording the video, I finally noticed the error:
Instancing: Property 'unity_LODFade' shares the same constant buffer offset with 'unity_RenderingLayer'. Ignoring.
UnityEngine.GUIUtility:ProcessEvent (int,intptr,bool&)
Looks like there existed similar bug just the other way around and presumably was fixed on 6000.0.21f1.
My is 6000.0.26f1.
At first, I noticed that almost all my LOD groups stopped working at build, then after some digging, I found out that they stopped working after changing the scene file and nothing else, not sure what particularly caused this, there were a lot of changes.
Interestingly the LODs made with Amplyfier always show all levels active while the LODs made with PolyFew show only the last level.
Edit: I tried upgrading to 6000.0.32f1 without rebuilding the library and the problem still persists