Asklemmy

Vintage Story is a slowburn survival game with a Linux version from the developers, not a compat layer. It's focused on realism.

Ranch Sim is a game in which you design your own ranch.

Starship Evo, formerly Sky Wanderers, is still in development but has reached a very playable stage. You build bases and ships out of predefined shapes but with highly variable scaling, as in ranging from 12.5cm grid up to 1m with all the standard slopes, panels, etc. It has logic systems, inventory and production systems, and control systems for space ships, hovercraft, mech walkers, and space stations, all using that heavily customisable building system. Then you can fly around doing little missions, trading, space ship combat, etc.

Archean is similar building but with more realism and programming but more sandboxy with no NPCs.

I've heard some good things about Steamworld Build.

I have heard someone say Icarus was like Ark but better.

7 Days to Die ticks much of those boxes as well.

Stationeers is another struggle, survive, thrive game with very realistic mechanisms.

Foundry is Factorio in 3D. Satisfactory is Foundry without a Gödel grid.