You do know that nothing's quite as funny as a trauma to the groin, right?
But I do agree - a game should not require the use of external software to solve internal puzzles. If I want to beat my head against something, I'll head over to Waking Titan and try to puzzle out what Hello Games is up to next.
This isn't to say there isn't a place for good in-game puzzles and the use of in-game mechanics to solve them - the Guardian Sites and Ruins are a great example of doing things in-game with in-game resources. Likewise the signals sent by various stations, and even NPC interactions like the "Follow my wake" interactions during some bounty-hunting missions, or the Scan-the-Data-Point to Find-the-target interactions are all means by which we can have in-game puzzles to solve without having to rely on steganography.
Even the holographic billboards at stations could be used to generate clues, by dropping in single-frames, or very short frame sequences containing clues and keep the games puzzles and solutions entirely in-game.