Solution is fine for me from a usability point of view.

For other users, it is not fine because they will first have to find this
solution, which probably will not happen before having fallen into the pit. So I
would prefer a changed default behavior.

I will try to convince the authors of the OpenPGP standard to remove some of the
complexity of the standard as well as the resulting issues.

What about adding an option to not embed the filename even if a file name was
given? It can be hard to convince other tools (e.g. enigmail) to use pipes for
just some of the operations ("cat %f | gnupg" for encryption, but not for
decryption). My workaround with --set-filename "" did not lead to problems yet,
so maybe this is good enough, from a usability point of view. Also, I just had a
look into RFC4880, and it seems that zero-length filenames are perfectly OK:
"This may be a zero-length string."