Just to clarify further.
You always pay essence when you install an augmentation in your natural body.
You always pay capacity when you install an augmentation into a valid cybernetic device.
You have to pick one of the two.
For example the low light vision eyeware augmentation always cost 0.1 essence (modified by grade and qualities etc) in case you install it as a modification to your natural retinal. But if you already replaced your eyes with cybereyes then it always cost 2 capacity of the remaining total capacity your cybereyes have (you already paid for the essence cost when you earlier replaced your eyes).
Eye-ware is either installed in eyes taking up essence or your cybereyes taking up capacity (low light vision, for example, can never take up capacity in your cybernetic torso shell or your cybernetic arm).
Same with ear-ware. They can either be installed in ears taking up essence or cyberears taking up capacity, but not in other cyberlimbs.
Head-ware is either installed in your head taking up essence or in a cyberlimb taking up capacity (any cyberlimb - not just cyberskull shells, but only if the augmentation have a listed capacity).
Body-ware is either installed in your body taking up essence or in a cyberlimb taking up capacity (any cyberlimb - including cyberskull shells, but only if the augmentation have a listed capacity).
2. Why is smuggling compartment listed in two different sections with dramatically different capacity costs ([2] vs. [5])?
They have two different sizes.
The smaller smuggling compartment that either cost essence or 2 capacity in a cyberlimb can only hold small or mini-sized items. Weapon size nothing bigger than a light pistol.
The larger smuggling compartment that cost 5 capacity (and can never be paid for with essence, it must always go into a cybernetic limb) can hold something the size of a heavy pistol or small SMG (this last part seem to have been lost in translation from 5th edition, but costing more capacity I guess is a clear indication of that it can hold bigger items....)