He does this by pointing to the allusions and references they use and the clear contradictions within them - often inversions of meaning from the original sources that are alluded to. Socrates makes these errors, as does Machiavelli. If you assume the errors are mistakes, the work's apparent conclusions become more shaky, but if they are intentional puzzles, the work gains additional meaning. We often use puzzles as teaching devices and writing isn't really different in that respect.
It's not really different from reading for literary subtext, it just applies that toolbox more widely. I believe it's more useful for writing than for reading because esotericism makes it easy to encode something legible only to intended recipients. I would not expect to parse new wisdom from the utterings of a CEO, as in article's example, until I become familiar with corporate culture in general.
My understanding is that Discourses on Livy is far less esoteric, though. It doesn't surprise me that particular works are esoteric, but does Melzer successfully advance an argument that entire bodies of work or even an entire era should be approached that way, without needing to evaluate each text on its own?