My first thought on this would be that maybe it's supposed to be that way in that Cyberware is potentially temporary, although the only definitively temporary Cyberware is really a skill chip, so I looked at the official PEG forms for guidance on that. While not directly answering this scenario
Clint did essentially answer this in that Attributes from Cyberware, not Skills from a skill chip, CAN be used for permanent Edge requirements. So that says to me the same should be true on reducing skill costs as well. Maybe CC can look at fixing those up for us in his next update.