Spotlight can't open a folder inside ~/Documents/
There are two questions here:
Firstly, Spotlight always sending you to ~/ (and not the folder you asked for) is I believe a bug.
Update: I have a MacBook running macOS 11.3 beta1. On this the search behaves correctly and Finder opens in the expected folder.  So, it seems this bug is being fixed.
Secondly, my interpretation of permissions for ~/Documents is that Big Sur has taken control of the Documents folder and won't let you make changes.  Unix style permissions and ACLs are overruled by macOS.
There is other evidence for the special role of ~/Documents.  Finder now shows subfolders that are not really inside the Documents folder.  These are folders belonging to some apps using iCloud for document storage.
There seems to be no way of turning back the clock and restoring the behaviour of Catalina and older.  This is just an example of Apple gradually taking away the freedoms we have come to love in macOS.