Exactly. I have the broadly same issue with my doctorate: I know essentially what I showed, but I only ever really completely understood my thesis's more abstruse passages around the time I was writing them (and being examined on them). But I don't find this surprising or concerning. The overriding motivation for doing a PhD was to try to contribute some original knowledge and insights to a field I find interesting. All this article talks about is, what did my PhD do for me personally, and tangentially how can the PhD experience help to train the mathematical brain. To me those are secondary issues, my reward is that my thesis, although hardly earth-shattering, gets checked out of the library every so often, and I get emails from interested and interesting people asking me about it.