BEE falls solidly into the category of interfering with 'natural' economic processes.  I do not wish to debate its laudable aims or whether there is another mechanism to better achieve this but it is particularly onerous when it involves high tech projects.  Let's face it, SA does not make trains.  You could subcontract some of the wheels or chassis elements but we don't do the expensive traction motors and control systems.  Even then, those bits that you subcontract will be more expensive.  Let's look at higher tech examples: what happens when SAA needs new planes or CSIR needs a new supercomputer?  Yes, SA does make some sophisticated antennas and composite cabin structures but these would constitute far less than 1% of the price tag.  On supercomputers – zilch.
They only way BEE can be introduced into such a contract is as a rent seeker.  They add zero value except their BEE rating.  This is not even Economics 101, its Economics 001!