As i see, most of issues is related to native extensions ? So it belongs to another issue instead of just packaging tool ?
Packaging pure Python often boils down to where to place the packages, the hierarchy between them and where to find the starting point for an application (if it is one and not a library).
Insert native extensions into the mix and you get all kinds of issues.
Like, which library to link to? Which version? Which foreign function library to use? Will my Python version be compatible with that library? Et cetera.
Written by one of the maintainers of scipy