The problem is not in them not disappearing, the problem is when one message (aka low-priority hint) shows when another message (high-priority aka linting) is displaying (effectively killing the high-priority message). The way to prevent this is to check if there's any message displaying at all before messaging a low-priority hint (which ensures that an unimportant hint never replaces a potentially more important message/minibuffer-message).
From: pinkanon pinkanon <pinkanon.pinkanon@yandex.com>
Cc: "43813@debbugs.gnu.org" <43813@debbugs.gnu.org>
Date: Tue, 06 Oct 2020 10:52:23 +0300
It's not only minibuffer editing though. It could be just regular messages/minibuffer-messages from anywhere
else. For instance messages from a linter or some callback response from some connection letting you
know something's been set up. I don't want my low-priority hinting covering any of that up.
The messages displayed by minibuffer-message will always disappear
after the timeout, or when some input event arrives. So they cannot
be a problem in your application, I think.
If you do see some problems, could you show some simple example of
that?