A partial answer to your question is that the MacOS does some weirdness with
regards to "Containers", where the Finder or certain apps would fake various
home folders like ~/Documents containing things that are actually in
~/Library/Containers... and so on, though I've seen even the Finder sometimes
shows the same folder as being empty or non-empty depending how I get to it. I
encountered this due to strange behavior I observed when migrating from one Mac
to another.
As to your question about moving this BBEdit folder to the trash, well you can,
but you would probably lose some BBEdit settings in the process, and the folder
would then get recreated for fresh settings.
I feel your best bet is to just take it that this folder is a standard part of
how the MacOS works, leave it alone, and organize your own files around it. For
example, if you used to organize your files within various folders directly
under ~/Documents, then instead make a new "top level" folder like
~/Documents/Foo and put your organization under there instead. Treat
~/Documents as if it were your root home folder ~ where the MacOS organizes it,
and have your own organizing scheme under the Foo, where you can expect nothing
else would mess with it.
-- Darren Duncan