I make different observations (using self-compiled gpg installed to /opt/ gnupg/master with a non-standard GNUPGHOME):
It turns out the source of the trouble was systemd, which was starting gpg-agent on demand, and was forcing it to use /usr/bin/gpg-agent. Setting a user override file fixed the behavior.
Really annoying to hunt down, though. My thanks to Phil Pennock for helping me debug this.
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