This is not a defect in functionality, only in the documentation
AFAIK. Find attached an Org file I used to tangle up the question
posted at https://emacs.stackexchange.com/q/56155/15483 .  At the time
I posted that question to stackexchange, I thought it was a behavioral
defect or a user-error on my part. Instead, now I think it is
something that needs improvement in the documentation.

The attached Org file launches an emacs -Q session as a child process
with a separate ".emacs.d" with nothing else in it, to guarantee it is
not polluted with my own special config.

The essential issue is this: The paragraph at the very bottom of the
Structure Editing page of the manual is misleading: It leads a user to
believe that all of the commands use the Transient Mark region, but some of
them do not or should not.  One possibility to fix this is to mention,
inside each described command in that page, which ones respect the
region, and which ones do not, possibly using footnotes for more
details.

Thanks to the Org contributors for a wonderful tool!