In distutils2, 99382aafa4c5 forces scripts to always be rebuilt and 463d3014ee4a goes further and deletes the whole build dir to avoid installing scripts built from a previous build call with a different configuration (i.e. different list of scripts).

The same issue may affect other build commands; if a module is built and then removed from the source dir and setup.cfg/.py, I think the install command would still install it.  The dependency code should take setup.cfg and files referenced from hooks to decide if the source is newer, and it should delete built files for which there is no source.