Mindustry is Factorio + tower defense. I haven't actually played Factorio so I don't really know how they compare, but because Mindustry has discrete levels my guess is it's "less good at the thing Factorio is especially good at". But I liked Mindustry a lot. (At least its Erekir world, I didn't play Serpulo.)
Previous list of puzzle games, +1 to A Monster's Expedition and Baba is You.
Previous recommendation of Understand, but I haven't played that myself.
Thematically I think Heart of the Machine would be an appropriate mention: it's a strategy/RPG game about being a fooming AI. However in terms of game mechanics it's a bit of a mess.
Almost all Paradox games would probably deserve a mention for being complex systems you have to actually interact with and understand. Shout out to Stellaris as the most accessible one and the one with all sorts of transhumanist stuff in it.
I like everything recommended above and in the current comments, so I'll add more that weren't mentioned although some deviate a bit from being "rationalist" focused:
I would throw Cyberpunk 2077 in there too actually, not so much for the mechanics as for the world and how the game invites you to engage with yourself.
I’d add Blue Prince to the list. I haven’t seen a game with so many layers before. It’s a masterpiece. I have 125 pages of notes, that I used to complete the game. Room 46 is just the beginning.
Timberborn would be an honorable mention. It’s a city builder game with beavers and water physics.
I endorse every recommendation you give. I'll add one for Offworld Trading Company, which teaches aggressive minmaxing and adjusting your strategy in real time in response to changing conditions; and for The Witness, which is insight porn but doesn't teach anything.
Here are a couple of specific comments on the games you listed and what they teach you:
I think Slay the Spire is an important rationalist game. The game punishes every bad decision, often in ways that you don't necessarily notice at the time, so it's easy to get to the end of the game and think "oh, I was just unlucky", whereas in fact it's very frequently a skill issue: spending more time thinking on any given move will almost always increase your win probability. You have to be constantly on your guard against: doing something that's "ehhh probably good enough". If you can win every fight with one more HP, that's at least 30HP saved over the course of the game.
Factorio teaches the skill "address the bottleneck". Again, it's quite easy while playing the game to end up running around tinkering at the edges, or performing processes manually, ultimately wasting a lot of time vs the correct answer of rearchitecting to improve some component by orders of magnitude. You have to be constantly on your guard against: sinking into the pattern of maintaining systems by hand.
Following is a list of games that, if you are reading this, you might enjoy. They're the hits, the ones that people repeatedly bring up and discuss, but no one seems to have troubled to write down. I'm sure these are all well known, but you could be in the lucky ten thousand.
Factorio
A massive logistical sandbox. Scratches the same itch as coding, but with supplies and engineering instead of code.
Universal Paperclips
A 6-9 hour free clicker game. At last, you can play as the paperclip maximizer from Bostrom's classic thought experiment Don't Create the Paperclip Maximizer.
Outer Wilds
An exploration and puzzle game. Once you get past the awkward spaceflight controls, the puzzles and storyline of this game work better than I've ever seen done elsewhere. Avoid spoilers or any info at all before playing this one.
Slay the Spire
A highly tuned solo card game. The combos and interactions will have you scratching you head, and the random possibilities will keep you coming back for more. Invented the genre of roguelike deckbuilder.
Kerbal Space Program
An accurate simulation of a space program and spaceflight, while forgiving enough to make the whole thing fun. You will learn orbital mechanics.
More Games
I'm getting a bit more subjective here, but there are all worth your consideration. Let's have more in the comments!
Opus Magnum / SpaceChem - coding oriented puzzle games from Zachtronics
Return of the Obra Dinn / The Case of the Golden Idol - anthologies of whodunnit puzzles with a unique perspective
Dwarf Fortress - simulation of a colony of fantasy dwarves. Intricate, chaotic, and frequently hilarious
Baba Is You - block pushing puzzles where the rules of the puzzle are also blocks to manipulate
Planescape: Torment / Disco Elysium - RPGs grounded in conversation, not combat
HyperRogue / Patrick's Parabox / Manifold Garden / Braid / A Slower Speed of Light / 5D Chess With Multiverse Time Travel - games that play with stranger forms of time and space