Is he really claiming that the manual (slit-on-back-of-box) Rising Card is his invention? It sounds like he's actually trying to import the idea that he invented it as a "third variation" just to fool them.
That's ridiculous, of course. There are demos of the rigged box that date back seven/ten years and I'm sure it was in books before it hit the internet.
I think the "trick" here is that he performed some stuff that's pretty standard fare and regardless of which solution they observed, he can just say, "Ha ha! I didn't use that method at all." In their first season there were a couple of times when Jonathan Ross declared them fooled because they surmised one method and the conjurer had used another. I thought that was a bit of a reach; this is even more so.
This is just post hoc face-saving. Maybe he was getting negative comments and his big concern is his book sales so he felt he had to find a way to claim victory. He was there to sell the sparkler trick. It's pretty good but obviously requires a special deck. Whether he really ditched in the two obvious ditches is not significant. The point is that even if they caught the wrong ditch, they know how the trick was performed. When you have three or four solutions for a particular move, unless your performance is themed "Figure out which slight I used along the lines, there", the issue is knowing how the effect came about, not which of the methods were employed.
Magicians may differ; this is obviously my lay person's interpretation.
The most important element, though, is that it's disingenuous to say you just wanted to be polite. To Penn Jilette? The guy makes his living calling things ********. (censor-speak for bovine feces) The show is about fooling Penn & Teller. Numerous contestants have disputed their findings and they've acknowledged them as "Foolers". If the solutions were conceptually/philosophically different from P&T's answer, the "man in the booth", who's a respected conjurer, can re-confirm. Aren't they required to explain the trick to that guy ahead of time? I can't find anything on the protocols of the show.
It's possible he was jerking them around. I remember seeing the episode and wondering why he was doing mundane stuff like the Rising Card, when they've seen that five thousand times. Ditto the deleted trick. It's just a variation on a trick done by every Harry Anderson barroom hustler in the world. I think it was deleted because it was such standard fare. Again, "here's a trick that others perform one way or another and I've chosen a third" doesn't "Fool Us", unless the bit is put forth as "Seemingly Boring Stuff That You Won't Be Able to Figure Out How I Performed". When P&T do those kind of tricks in their shows, they reveal to the audience where the hanky and panky took place. If that was his intent, then his judging session should've included that.