As I mentioned in chat, DROD does better here, perhaps setting some kind of record (if you don't count games with no crates at all -- yes, they do exist -- as having an infinite score).
The attached picture shows the first appearance of a crate, four minutes into The City Beneath. But this game is a direct continuation of the previous game, Journey to Rooted Hold, so perhaps it would be fair to include the time taken to play through JtRH in its entirety -- which, on my most recent playthrough, was twenty hours.