If you add it to gpg.conf the Pinentry won't be used and there are fir sure
cases where things won't work. In an unattended use I can't see a problem right
now.
We can't change the behaviour of --passpharse-fd; it is widely used and:
if ( !opt.batch && opt.pinentry_mode != PINENTRY_MODE_LOOPBACK)
{ /* Not used but we have to do a dummy read, so that it won't end
up at the begin of the message if the quite usual trick to
prepend the passphtrase to the message is used. */think would break or - worse - may insert the passphrase into the message.
The passphrase is still used for symmetric only encryption in batch mode.

