I've noticed a seemingly miraculous reversion once or twice. In the case of folder in which I had organized my icons just the way I wanted, at one point, the view settings got scrambled, the icons got scrambled, and I figured that was that, I'm screwed. But a few moments later --not sure what I did, possibly closed and re-opened the window once again, possibly fooled with the view settings-- the original icon arrangement reappeared.
I'm not sure I have any folders arranged in recognizable ways that go back as far as OS9, but I definitely have the impression that the view-setting-scrambling affects older folders less than newer ones. When a newer folder gets hit, there's nothing left of the previous view. I would only notice in the cases of folders I've set to icon view and arranged the icons per my workflow. For an older folder, in my experience, the icons settings are stable or nearly so. I think I've seen a few icons shift around while most stay as I arranged them.
As for "other repositories" of window settings... I think Finder knows nothing at all about folders that it hasn't been told to open for a while. When you open a folder, Finder almost certainly reads .DS_Store and displays the folder accordingly. Probably when you close that folder, Finder saves the settings back to .DS_Store.
Let me make some wild-*** guesses about some of the details:
a) There are multiple versions of the .DS_Store file format over the years as the Finder has evolved, and
b) the read step transforms the information in .DS_Store to a convenient in-memory format, and the write step transforms that format back to the latest .DS_Store storage specification --or not, possibly, for older folders; and
c) that there's some amount of buffering going on.
I think that a relatively minor glitch in any of these steps could scramble view settings. For example, a problem with the buffering could account for the apparent reversion you and I have seen. (Buffering problem? Might look something like this: the in-memory copy should be erased when the data is written back to the .DS_Store file but isn't.) I'm suggesting that there probably isn't a completely separate method of recording view settings, just a problem with managing the data that originates in .DS_Store files and gets written back to those files.