The custom chipset as well as RTG form part of SAGA. So right now there already is a part of SAGA implemented in the public version of the apollo core.
However, SAGA will be more than just AGA+RTG. As already pointed out the hardware registers for controlling the RTG part are mapped in the same address range as the amiga hardware registers. So chunky modes could be controlled by the copper (or a new copper) just like the planar modes. This is where SAGA begins to offer something more than just AGA+RTG. There are many ideas for additions to AGA such as a HAM10 or a 10-bitplane EHB mode. In any case AGA compatibility should be a first objective before new features are added. But, for example, when you design the bitplane DMA mechanism, it doesn't mean more complexity to fetch a maximum of 10 bitplanes instead of 8. So you could just prepare everything for 10 bitplanes even when you haven't implemented any sprite engine yet and so on. So sometimes it may make sense to add new features even though you haven't achieved 100% compatibility with what's there already because the new feature is basically available for free.