I'm afraid I don't have the maxed out 2016 to test (much as I'd love to!) But it does seem very unusual.
Not sure if it'll work on your model but try testing by forcing both iGPU and dGPU in GFXCardStatus:
http://gfx.io/downloads/gfxCardStatus-2.3.zip
Also leave it on 'auto' and see if VLC activates the dGPU?
So basically we're verifying if VLC uses discreet graphics when it's running and if the problem persists with both integrated & discreet. Hopefully this'll isolate where the issue lies.