That patch was mainly about MP play, hence no wormholes are wanted. Those things are to level the maps for all human players. No black holes means player A is not handicapped with them while B does not have them.
Same for wormholes and planets in home system. If A gets 4 planets and B gets 1, A has an advantage. If you can make it so all home systems have the same number, you make it closer to even.
I don't know all the fixes, but I doubt they make a big change to the games. The thing is casual players that just want to relive the old days may want all the warts as part of the charm.