That discussion has come up in the past on the Hero Lab forums.
If I recall correctly, the argument that he has is that modifications require you to open up the device and play with the electronic "guts" which is arguably very hard to do with an implanted device.
On the other hand, however, you could conceivably make all of those modifications and then implant the device.
My best suggestion for a counter-argument is this: The rules never explicitly disallow this action, if an action has potential table-variation the program should allow the broadest application of a rule and leave more restrictive applications to individual judgment. If it could be possible, but some games might not allow it, Hero Lab should allow the user to do it, and let the games that don't allow it to simply not do it.