I put together a tool called Setl a while ago to fix some of my workflow problems around using Setuptools in a pyproject.toml project, and one of the features I implemented was to reuse the environment during builds to avoid re-installing build requirements. My usage is likely far less sophisticated than scikit-learn, so there should be many rough edges to deal with, but I’d be extremely glad (honoured!) if there’s interest to help me improve it.
Regarding pip install -e though, this kind of feel like an A-B problem to me. Why does Cython think the Numpy files changed? pip currently sets mtime for wheel contents (if possible); what can it do to convince Cython the Numpy copies are the same?