That's kind of the intent of Project Sisyphus as well, or at least the second act.
I think, when doing that kind of thing, if you want it to remain a role-playing game and not accidentally turn into a board game, you probably need to resist the urge to have explicit mechanics for everything. Here, you definitely want to have rules for some things, like powering systems and how long it takes to get around the ship. But if you don't want it to play like a board game, I would suggest leaving more room for the Warden to interact with the players, instead of both parties interacting with the game mechanics.