As a result, the SEC does not allow anyone to run an exchange that trades those illegal securities.
Being a registered security isn't hard, all sorts of stupid and speculative instruments get registered. If your shitcoin isn't able to get registered, the fault is with it, not the SEC. If your exchange isn't allowed to trade that shitcoin, the fault is with the coin, not the SEC. It's not the SEC's job to provide guidance on how to run an exchange that trades in unregistered securities. The only guidance it should provide in answer to that query is 'You can't.'