Thanks werner -- I've filed an upstream issue to bring awareness of the change
to the software I use that was affected (duply/duplicity), I'm sure this is
going to pop up for others as 2.1 becomes more widely adopted. Maybe add
something to the release notes or docs for '--passphrase-fd 0' so folks know a
config change is needed in their apps and gpg-agent? Regardless, I appreciate
your help.

(marking as resolved)

Roger that, thanks - I've tested it on a VM with my keys and things seem "like
they used to be" for scripting an automated passphrase entry. I specified them
in my ~/.gnupg/pgp.conf and ~/.gnupg/gpg-agent.conf since editing many
individual softwares is not possible at this time, it needs to be backwards
compatible.

What side affects (breaking things?) does having these options permanently
enabled in configs are there? Having the allow in gpg-agent.conf is harmless,
but what about the client side gpg.conf?

If client gpg '--passphrase-fd 0' is useless without '--pinentry-mode loopback',
why not make this an automatic added option (internally) if '--passphrase-fd 0'
is specified? Of what use with gnupg-2.1.x is '--passphrase-fd 0' without
'--pinentry-mode loopback'?

I double-checked the official docs, there's no mention of needing these new
loopback settings in the section for --passphrase-fd 0:

https://www.gnupg.org/documentation/manuals/gnupg/GPG-Esoteric-Options.html#GPG-Esoteric-Options

"If you use 0 for n, the passphrase will be read from STDIN." (but as we know
here, it's not unless the new loopback options are added)

A few Arch users are reporting the same regression/breakage, thread here:

https://bbs.archlinux.org/viewtopic.php?pid=1479136