Your argument seems to be "reusing trading-card code for a currency exchange is stupid and would result in a terrible, bug-ridden product." Mt.Gox is terrible and bug-ridden. I'm not clear what you're disagreeing with.
We cannot know what was reused from what, absent new evidence, as there is no public example of an actual MtG trading card site that I can find anywhere, just a quick note saying that the idea was "patent pending" and that one might someday be found there until a Bitcoin exchange popped up.
I would be quite interested if anyone has new evidence. The record, so far, is a bit thin. Perhaps the Jed McCaleb has a Github or other public repository containing items of interest?
Before the Wired article, the Wiki article implies that the site was an operating Magic card exchange, but the citation is a link to the Internet Archive's copy of the stub page, with absolutely nothing there to substantiate the idea that it was actually an online exchange. The Wired article appeared later and is unsourced, but could plausibly have taken the Wiki article's unsupported statement at face value. Then just the other day (February 9) the Wiki page was edited by a user named Agyle to use the Wired article instead of the Wayback Machine reference.