I'm pretty sure the two are related, no? A B-trees is a disk-friendly structure (shallow and wide), skiplist aren't (but they are a concurrency friendly structure)

Right. My point is that "you can't use atomic instructions with disk-backed databases" is oversimplified to the point of being incorrect: it's wholly feasible for, say, Postgres to implement a skiplist-based index (or some other lock-free data structure) while still backing its store with the disk, with the only downside being a performance hit if working memory is not large enough.