I'm not sure you've understood. All bugs with combined layer and custom terrains should be fixed now, so there is no reason not to use them. If you still encounter problems (and it's not with worlds, terrains or layers created in versions 2.3.0 through 2.3.3), please let me know!
I never really got them to work as I wanted anyway.
If you think there are bugs with them, please report them! Regarding multiple layers: they are still applied one at a time; could it be that earlier layers are placing so many objects that there is no more room for later layers to place any?