Is it safe to save things inside of /Users/<user>/Library/Preferences ? It seems like any application can just create any file in this directory. Do we have any guarantees from Apple about the security of the files placed here from our application?

If you’re worried about cross-app access, you might want to take a look at https://developer.apple.com/library/archive/documentation/Cocoa/Conceptual/UserDefault[…]ngPreferenceDatainiCloud/StoringPreferenceDatainiCloud.html

yes - that's what I am worried about, but storing in icloud / non-locally seems like a bad solution also. Is the idea that apps can just easily access other apps preferences?

You can read on what is available at https://developer.apple.com/documentation/security/app_sandbox

If you opt in to the app sandbox then you can store files that are protected from other sandboxed apps but not other apps in general.