The actual heritage is when `ls` was written to exclude .. (dot dot) directories from it's listing the code literally just had the logic to exclude any files which had a dot/period as its first character. Later operators exploited that bug/feature to create items with a dot prefix to make those files and folders hidden. Eventually this became convention.
Whereas systems released more recently understood the need to have a hidden file attribute so made it a first class property.
I do love POSIX and often the first to defend some of Linux or BSDs idiosyncrasies but if there was ever anything that was worth someone saying "I know we've always done it this way but it's shit and it's about time we implemented a proper solution", it would be the dot prefix kludge. (I also know it's easier said than done and would take years for all the tooling to catch up)
Of course you do have system files, which are hidden from all standard folder listings, but aren't usually used by software, presumably because they're too damn difficult to find again (although I really hope google drive realizes at some point that desktop.ini is supposed to be a system file, not merely hidden).
https://docs.microsoft.com/en-us/archive/blogs/patricka/wher...
https://docs.microsoft.com/en-us/windows/win32/shell/csidl
.NET has its own set which is also very old and goes back to .NET 1.0 (as old as Win98) https://docs.microsoft.com/en-us/dotnet/api/system.environme...
