The mechanic of bionic implants using bodypart "slots" was introduced as a balance measure against hoarding implants. It appeared out of good intentions but is at best too shallow, and at worst unfairly-limiting.
It's also worth pointing out that at this stage implants all have no effect on the body: they add no weight, take up no internal volume, and don't add or detract from one's appearance. As far as the game's concerned, the implants disappear into a bag of holding from which they operate perfectly.
A better system would involve assigning layers taken up for each implant, as well as the volume of space they require and the weight they add. It could be implemented alongside full body simulation or the game's current treatment of creatures.
Each implant would occupy space in its own layer for each affected body part. Each layer, in turn, would offer overall volume that implants could occupy, set at two values: safe maximum, and strict or unsafe maximum.
Safe maximum demarcates volume within which installing implants produces no issues. Going past that creates constant pain, minor but compounding with further installations, as well as encumbrance and potential other issues.
Strict maximum is the limit beyond which further installations would lead to permanent damage to surrounding organs, as well as other severe penalties: encumbrance, disfigurement, increased risk of infection...
It may be possible to allow installing past the strict maximum for players, provided they agree to inflict mentioned negative effects upon themselves – making it similar in nature to the chimera mutation path. It should, however, be allowed on NPCs and monsters through random generation, especially those whose origins suggest surgical intervention.
Layers are not meant to replace bodypart-based bionic management but augment it. Used in conjunction, they can provide a deeper level of potential customization for a more precise, verisimilar experience. They're also meant to be precise, so that each potential bionic only uses the space of the part it's meant to modify.
This provides way for smaller, more specific bionics that have a smaller footprint on the body and the character's sense of humanity, without excluding potential comprehensive that cannot but require a large set of changes in order to be effective – e.g., muscle augmentations that have to fortify skin and bone of the affected body parts so that a sudden flex doesn't rip them apart.
See also: Cataclysm issues → Transhumanism rework proposal, part 1: Bionic slots
List of Layers
The list is comprehensive but perhaps not exhaustive. Some parts of the body won't have all of the layers available (e.g. eyes, hands).
for items residing outside the body part
e.g. eye protection lenses
bones, joints, tendons, ligaments
No matter how small, each implant must take space within the body once installed, unless it specifically and only resides outside the body.
The primary difference between slots and space is that space is more objective, being based on the final volume of the implant, than arbitrary points.
For sanity's sake, it should be assumed that, however the implants fit within the confines of their layers, they fit together well-enough that they don't cause collisions or encumbrance.
Using implant volume for space calculations would require revision of existing CBMs.
Some of them, like the internal chronometer, could be exceptionally small – the size of a pill, given that it's an advanced technological product – and taking barely any space at all. Others, like subdermal coating or skin augmentations, may occupy a small portion of all body parts.
Certain CBMs will have to be fleshed out in order to better understand their placement and space necessary. For example, grotesque bionics such as Aftershock's solar panels may be reworked into a more-subtle skin augmentation. The same could be done to alarm system, making the two compete directly, forcing the player to make meaningful choices.