[Q]

You are all right about the AI problem with the master computer after the new patch. But IMHO the solution is quite simple: make the cost of a master computer equal or less than a bridge plus one life support plus one crew quarter and the size equal or less than 30kT. Then it will not harm the AI to use the MC even for the smallest ships.
In my personal mod I went a step further and made the master computer technology a racial technology and this works very well.