Well, that is one of the core simplifications of Civilization game series as a whole, as well as many other global strategy games. Whatever government and economy type you are nominally running, your state always functions as a planned economy, with central government (you) directly dictating every city what to build and when. Almost everything is state-planned in Civ4 in all eras of human history. I only saw it addressed in a remotely satisfying matter once - in Victoria game series by Paradox. Even other games from the same company suffer from that - in Hearts of Iron series, no matter if you are playing USSR, Nazi Germany or USA, your economy will be 100% planned. So, bonuses for some civics in our mod basically try to account for "private sector" activities that happen independently from player's actions.