Typically games built with a goal of being easily modded often store data in plain text documents, such as Rimworld. I can't see why an entire database system would be implemented just to read a few saved variables in other games? Sure if it's more efficient or built into the engine there's likely no reason not to use it.
I'll focus on answerable bit of the question:
I can't see why an entire database system would be implemented just to read a few saved variables, but at the same time, if it's more efficient or built into the engine there's likely no reason not to use it.
You are missing the point. There is no real reason to invent bicycle (own DB system) when you can just grab some which is already field-proven and attach it to your game (custom engine or whatever). DB systems are typically 3rd party tools or legacy from previous games studio has made - they come at lower "cost" or free.
On the other hand - plain-text has following drawbacks, which contributes to its lesser use in app-making:
- it takes more space and is longer to read from HDD
- it needs parsing before it can be used
- it does not have random access (unless structured in some non-texty way)
However there are pros too:
- human readable
- could be tweaked with simplest of tools (Notepad)
Those pros come in handy when you need more editing and less playing (think Alpha-Beta stage). But they become drawbacks in Release. That is why some games support both text and binary, because the text has remained from early dev stages.