1. The MtG app was hosted on a subdomain (CNAME record, no A record) that sometimes had an accompanying apex-record lead-gen website to "sell" it, but usually didn't. (When you're an engineer making a webapp, writing the lead-gen copy is usually the last thing on your mind.)
2. The app subdomain served a robots.txt that prevented the Internet Archive from indexing it--as is usual practice with app subdomains.
3. McCaleb doesn't generally want to talk about how his site used to host an MtG exchange, because that'd make people less willing to take BitCoin seriously. He doesn't deny it, though, nor use the misapprehension as a source of humor in interviews. He just clams up.
I'm not saying gwern is wrong, but he hasn't inviolably proven his hypothesis yet, either. I look forward to a comment from McCaleb, if there ever is one. (My own hypothesis would support McCaleb never responding to gwern's query.)