I'm a simple man. Once the prosthetic limb was sourced, paid for (out the nose usually), and delivered; I changed the injury to a broken bone type, and overwrote the fluff text that the limb was cybernetic. Once the "broken bone" healed the pilot was assumed to be able to use without additional difficulty.
The cybernetic limbs were normally good enough to not apply penalties at the TW level, as they tended to be sourced from the best the IS could do in the time period (with appropriate CBill cost) along with keeping bookkeeping clean. But obviously if a wooden peg leg was attached instead of a state of the art cyberleg additional penalties could be applied.
