That seems likely the case. Plenty of tools enable copyright but don't do it for you. For instance, Blu-ray decoder applications generally can operate unharassed as long as people have to "find" the decryption keys elsewhere.
The fact that Popcorn Time comes preconfigured to find illegal content is what they're going off of, and it looks like in Popcorn Time's reply, they're claiming the removal of those specific configuration files, they want the repository restored.
As usual, I truly love GitHub's policy about handling these complaints publicly, they offer so much direct value in being able to see the process and procedures outside of any sort of NDAs.