The queue_runner process belongs to WooCommerce. Nothing wrong with that, but what’s odd is the fact something is invoking a tracing process. It might be due to Query Monitor, I’m not sure. In any case, while tracing may degrade overall performance, it would not affect the SQL load. The fact that the queue_runner process timed out only reinforces the fact that something is taking too long to execute. We already know that ??
You have SQL queries taking 3-6 seconds?? That is a very long time for a query to run! They usually run in the millisecond range. For example, all 30 queries on my test site took a total of 0.100 seconds to complete. My test site DB is relatively small, so it’s not realistic comparison. The point is that 6 seconds is orders of magnitude longer than expected for a single query.
Please post the SQL of a couple of the queries that took such a relatively long time.