Caused by 133dde41bb, it is expected behavior now for linked ID in
general, see also #105786 and #106321.
However, Scenes are a special case here, since they are almost never
(and should not be) indirectly linked by other data, and have (almost)
never any real user, unless they are active in one of the open main
windows.
So this commit essentially reverts the new behavior implemented
in #106321, for linked scenes only.
Should be backported to a potential bugfix release of 4.0.
60a9c8ee25