I praised the conversation with the broken hologram guy, but that’s because I have the hindsight of multiple playthroughs. He was actually really irritating on my first trip through the game, which is arguably the most important trip.
The idea of “these details seem dumb at first and only make sense after a later reveal” is a really dangerous game to play. It’s bad enough in a movie, since the audience can lose their trust in the storyteller long before the reveal. But in a game? Players will likely have many hours of gameplay between the seemingly dumb stuff and the payoff. They will very likely have breaks between game sessions to think about what the story is telling them, and thus lots of time to dwell on the apparent problems.