This is probably an unsatisfying answer, but simply put, a lot of systems these days are just bloated. I'm not only talking about the OS/programs running (though it often contributes), but rather the creature comforts developers have taken on over the years in the name of productivity. In fairness, the scale of recent games wouldn't be quite so possible without our superfluous tooling, but it definitely comes at a cost. A great example is Minecraft, which was originally written in Java but later ported to C++ for more consistent performance. Java's extensive library support, object-orientation and quick-and-dirty graphics access made it a great tool for prototyping, but when it came to delivering a high-performance product it often fell short. There are many such anecdotes in the gamedev community, so choosing the right tool for the job is hugely important.
Dwarf Fortress and Rimworld are both interesting topics on their own though, and while I'm dreadfully underfamiliar with their codebases I do love the games to death. I'd guess that if you profiled them, the heaviest slowdown would be accessing/manipulating memory with hundreds of values across thousands of instances. Both games are extremely heavy-handed in their approach to simulation, so it wouldn't surprise me if that constituted the bulk of their usage. Dwarf Fortress itself is an interesting case study though, because it's world generation can take hours. As more years pass, it takes longer to generate, which is probably a testament to how many interconnected pieces it's weaving.