I like both "That, That Is" and "Mind Drive" from the Keys sessions. To me, they're both modern epics worthy of inclusion on lists along with the classics from the 70's. No, they're not going to beat out "Close to the Edge" but I do put the Keys tunes on sometimes.
That said, I agree with you that the lyrics to "That, That Is" are pretty weak (as opposed to "Mind Drive" which are just incomprehensible). I think the problem is that Jon was trying to actually convey a message, but his literal lyrics aren't nearly as good as the nonsensical stuff, which at least provides some neat verbal imagery. And yeah, the title is kinda dumb, too. I think it would be greatly improved by simply removing the comma. "That That Is" actually makes more sense. The song is about things that are. Simple as that. The comma makes it all awkward and is grammatically incorrect in the first place. Between that and the "crack time" lyrics, I can see why people don't love it.