GCS is correct. You still have the disadvantage, you just don’t get the full point cost because something lets you offset most of the downsides.
A good way to look at it is the most common mitagator in any setting: glasses. A character wearing glasses still has Nearsighted or Farsighted, the glasses don’t change that. But what they do do, is allow the person wearing them to avoid the downsides of that disadvantage.








It isn’t really an “upside”. ST, for example, has multiple components to it. It improves your lift, melee damage, ability to break out of binds, and hp. You can buy all of those individually. In this case, having bionic arms means you’re effectively able to lose levels of Arm ST, which is normally 5pt/level. You can also effectively lose any DX skills which use your arms, which is most of them.
Ultimately as gamemaster, it’s up to you to decide how likely this is through emp, rival hackers, corpo sabotage, ect. The discount remaining is to account for the possibility of it happening.