From experience on sites with both
windows as tag names, there's a lot of confusion. So let's avoid this pair.
For the operating system, microsoft-windows is the obvious, clear alternative.
For the concept, window-manipulation and window-decorations (or window-appearance?) cover most topics (I don't expect window-management to be a distinct thing from window-manipulation on this site) but I don't find these to be great tag names. gui-windows doesn't look clear to me. Better suggestions are welcome (I might steal them for U&L).
Just having a tag named
windows is likely to cause misuse as people meaning either the concept or the OS will use the name without checking. So I propose to avoid this name altogether. It is possible to arrange for a popup to appear if someone tries to use the tag name
windows, with a message saying something like “the name
windows is ambiguous, use microsoft-windows or window-manipulation instead”. This needs to be set up by Stack Exchange staff.