To me it seems more sensible to store information relevant only to this OS in a specific cache somewhere within that OS. It would even make cache-like functionality such as evicting old entries super easy.
There are some tradeoffs. Like if you used a usb and set up folder colours or any of the other things stored in the file, they would not move along with the usb when used on another computer.
If I set a folder colour in Finder on my work MacBook, and then plug that USB drive into my personal computer which uses Thunar as a file browser on Debian, nothing would happen.