Weird, I rebooted and now it works...

Interestingly, gedit seems to run find with sudo:

This doesn't seem to be causing an issue now. It can be closed, resolved.

This seems to have been resolved in the intervening period - due to updates I guess.

Actually, this bug doesn't just affect alt-menu symlink creation - anything done with a nautilus alt-menu is affected and kills nautilus (even simply clicking outside of the alt-menu)

Hmm, okay - I've just checked my little local CentOS server and indeed, it doesn't have a gpg.conf (or any conf) under ~/.gnupg. My apologies.

No, that is not the issue here. The issue here is:

So, if PureOS insists on being unusual, the question becomes - why is PureOS unusual in this particular way?

Phew, this file exists on the gnupg implementation in Debian, CentOS and Fedora, at least - those are all fairly standard implementations of gnu/linux (although arguable implementations of two standards).

man gpg says:

I'm not sure I understand the relevance of the answer to the question?
The question was: why are the defaults not reflected here:

~/.gnupg/gpg.conf (as per man gpg) as I would expect and are on my Debian 10 install
Or;
~/.gnupg/dirmngr.conf (as suggested here)

Those aren't 'system-wide' locations.