gpg-agent (I tested 2.4.something) looks at /etc/gnupg/gpg-agent.conf according to strace. I'm not sure why you think it doesn't, but maybe your older version really doesn't.

I was asking because the question came up on NixOS and how we handle this, for us, breaking change.
We don't have a global PATH we could necessarily symlink into but a wrapper could work. NixOS also does not use the alternatives system at all because it wouldn't work well with the distro design.

The profiles are not any longer useful because global options are way more powerful (/etc/gnupg/gpg.conf et al.).