BMW was probably looking at the total cost to develop a new car and ways to cut out waste. If a variant of any product costs more in R&D then it brought in for revenue any business would be cut it. You would in effect be making more money while doing less. Going beyond the R&D costs the less variants you have in your product line means you have a smaller supply chain, and so on. The effects are multiplied throughout the company.
Again I've talked to people in BMW at length about this. There are plenty of enthusiasts that work there that want to see manuals in more cars but there has to be a business case. As automatics and flappy paddle transmissions get better and better fewer and fewer still want a true manual and the case to continue producing them gets harder and harder.
My E46 M3 Rebuild Thread