Cubik Studio

Location: Model properties dialog in "Minecraft" tab
Option name: Split into smaller Models
Option type: Checkbox

Option action when enabled/disabled/clicked:
enabled: splits model to smaller 1block models on export
disabled: would not modify model export

Why do you need to save each element as separated models?

Not each element but it may be useful when you have a 1x2x1 Model (size in Blocks) split up into 2 1x1x1 Models.
As for example when you make a mod with a 2 Block height block you might need 2 Blocks for that and 1 of them would need to have an "empty"/"invisible" model.
Generally all 2 block tall minecraft blocks are split into 2 models see the tall flowers.

I see. That will need to wait the groups feature then.