The notice of future deprecation can be safely ignored as long as you aren't bumping your minimum requirements.
The issue with `$prefix/lib/x86_64-linux-gnu` is because there's a Debian quirk. For both autotools and meson, the default if not specified is `--libdir=lib`, however, only with Meson that default changes to the directory output by `dpkg-architecture -qDEB_HOST_MULTIARCH`.
With autotools, the official debian package for geany instead just passes an option to `./configure --libdir='${prefix}lib/x86_64-linux-gnu .....` because they really, really, really want all projects to use that directory.
The user specified value `--libdir=lib` will always override that. But apparently it's considered a bad idea on Debian.