meson's setup.py file installs scripts with a python3 shebang due to broken hackery in the upstream setup.py script. I have reported the issue upstream, but we may want to work around it in the ebuild if they do not resolve the issue in a timely manner.
A fix was merged upstream. I think we can wait for a release to pick it up. https://github.com/mesonbuild/meson/commit/8b0d575823ca6a0a36c20952220b9beec6664b20
This is fixed in 0.41.0.