I don't know the exact answer to that question, but I assume that if you encounter it shiny first and knock it out, it won't be guaranteed shiny the next time you see it post-game. In that skarmory video, the person was battling Gonzap in the team Snagem base, which means he didn't snag Skarmory before the final Colosseum. If the skarmory was shiny during that first battle, I'm sure that another video would have been made. 