Yes, this is a key problem with pyproject.toml. It is actually not generic, the constraints you write in it are specific to how you build wheels for PyPI - they do not apply for other distros. This is not really documented anywhere, and widely misunderstood by distro packagers.
This is not a pyproject.toml (metadata) issue, but is because of build isolation. You can still have both here, just set your virtualenv up the way you did before and turn off build isolation with, e.g. python -m build -wnx.