> Moreover, some of these C++ exectuables depends on DLL which are only in the Scripts directory and it might not work.

In this case, perhaps these tools should be in a separate directory? A simple .py script could be added to Scripts that works with "-m" and launches the executable.

> I do not think that your proposal addresses the full problem.

You'll have to excuse us. We've had a lot of experience in this area with this problem, and so we'll be very quick to rule out imaginary proposals like the one you posted that we know are technically infeasible.