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The main issue is maintainability. Everytime a module is
added, a project file needs to be created, which is more
tedious than adding a few lines to setup.py (although one
also has to remember editing Modules/Setup.dist); in
addition, Tools/msi/msi.py needs to be edited.

Everytime a "global" change is made to the compilation
options of Python (e.g. adding AMD64 configurations), it
needs to be applied to all project files individually.