I don't think it would be possible for normal comments to reply to custom_json, at least without something quite convoluted, but that seems okay. If you want to make a normal comment you can go back to top level (or some higher level) to do it.
I think there might also be something for just deprecating normal comments altogether (if you want to contend for rewards, make a top level comment aka post). They have a high cost in terms of RCs/blockchain which seems perhaps just not worth it for the small number that get paid out and total payouts. Getting rid of all the comments would make posts significantly cheaper I think.
I wouldn’t want to see “full” comments deprecated. I think that would be negative toward multiple use cases, such as the increased engagement and reward mechanisms SteemPress is enabling on personal websites, or how it would cripple Quora style interfaces where answers and replies should be rewarded more than the top level question post.