Three first ones can also be game engine limitations. Im not saying its good desing and its always because the limitations, but there might be more happening under the hood that does not show to the end user. Things like quest stage flags or loading things behind the cut scenes.

Dialogue history i agree completelly. I love the way pillars of the eternity did this. I also loved how text refering to things like cities, characters and gods were highlighted and you could see short summary hovering your mouse over the higlighted text and clicking it opened the codex where you could read about the topic. This helped me immerse to game because my character would what the capital of the country is or what god uggapugga is. Also it helped when there was long times between game sessions.

About map markers. I like when i can add markers or text on the game map, but inherently i think game should do these things for you, either adding a symbol in the map, or adding something in to games quest log or codex. But on the other hand i lived in a era where if i wanted a map for game i needed to draw it by myself on the grid paper. The habit has stayed with me and in games like Dark souls, Remnant and blue prince i keep small notebook with me, where i write my notes and stupid theories. To me its really fun to read those scribles later and try to figure out what i have missed or how dumb i was.

Hollow knight, Project Zomboid, minecraft and Legend of Grimrock have all very different tools for you marking your map and in all of them the map system is part of the game desing and gameplay loop. While these games benefit from the map system to most of the games its just unnecessary. The ability to mark "digging spot #31" just is not necessary.

I love how in pillars of eternity and satisfactory you have in game notepads. And now days steam notepad is also great. You can even add screemshots to it, but i like my oldschool hand writing stuff more.