The word I heard was that NEBP needed fill from the dredging of the river and marina in order for the rest of the development to work, thus the desire to retain those parts of the plan. The upper Caboolture River around and downstream from the highway bridge is extremely stressed from sewage input and the NEBP development provides an opportunity to take the sewage water and use it on the golf courses etc, thus helping the upper river, which is presently extremely degraded (e.g. has a dead zone during the summer months with no oxygen in it). That and proper riparian rehabilitation in the area of the new development will be a very big upside for the upper/middle river if the development goes ahead. Downside is the dredging and the increased boat traffic potentially causing bank erosion and pollution from outboard/inboard emissions etc..
Deception Bay and Pumicestone Passage are already very stressed ecologically, so addition of many tens of thousands more people via developments such as Caloundra South will accelerate the degradation of these areas even further. While the proponents will try to mitigate some environmental impacts, the cumulative impacts still accumulate. Unless water quality declines at a whole of catchment scale can be halted and improvements can be made (lets get developers talking seriously about marine rehabilitation as part of these projects) , we will end up with poorer quality fish habitat, which will mean less fish and less biodiversity. Thats the price of "progress".