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.