“You Aren’t Gonna Need It” - one of the most important software principles.

Wait until you actually need it.

I interpret YAGNI to mean that you shouldn't invest extra work and extra code complexity to create capabilities that you don't need.

In this case, I feel like using the filesystem directly is the opposite: doing much more difficult programming and creating more complex code, in order to do less.

It depends on how you weigh the cost of the additional dependency that lets you write simpler code, of course, but I think in this case adding a SQLite dependency is a lower long-term maintenance burden than writing code to make atomic file writes.

The original post isn't about simplicity, though. It's about performance. They claim they achieved better performance by using the filesystem directly, which could (if they really need the extra performance) justify the extra challenge and code complexity.

Is this what we do with education in general?

100%.

Premature optimisation I believe that's called.

I've seen it play out many times in engineering over the years.