In this instance they were needed because the camera was moving... having the spikes on the greenscreen allowed us to lock the American flag background with the camera move. In this case After Effects used the marks to "learn" what the move was, and have the matted-in background follow the action. If it had been a locked-down camera shot, no marks would have been needed.
If you Google or YouTube search "After Effects tracking" you'll probably get tons of responses and tutorials.
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