While for a JPQL query, the SessionImpl call applyQuerySettingsAndHints, for native SQL queries this does not happen.
By calling applyQuerySettingsAndHints we could auto-apply query hints (e.g. query timeout), as explained in this article.
It would be great if we could set a global query timeout for both JPQL and native SQL queries.
More, after studying the code base, it looks like the applyQuerySettingsAndHints call is not consistently applied even for JPQL queries, and that should be sorted out as well.