I had this problem with earlier GPGTools, but this one seems ok. I did an install on a machine where I haven't had the old versions and the doctor is happy afterwards.

Ahhh. I rarely run brew doctor. Warnings aren't the worst things in the world though and I don't think it is unreasonable that they stick libs in /usr/local/lib.

I don't disagree but it does make it harder to debug other homebrew issues.

That's really Homebrew's problem. It's inappropriate for Homebrew to try to take complete ownership of /usr/local. That's what /opt is for.