I think the changelog is a bit confusing on that point. I interpret it as meaning that CTE is a default optimization:

"The default behavior was formerly NOT MATERIALIZED, but is now changed to MATERIALIZED for CTEs that are used more than once"

The default was NOT MATERIALIZED only because previous versions of SQLite didn't have this feature at all.

"now changed to MATERIALIZED for CTEs that are used more than once" means that the query planner DOES use this optimization by default if you don't do anything - the optimization only makes sense for CTEs that are used more than once in the same query.