At this time, the Average Time in Status Chart calculates weekend days and non-working hours (which logically include the weekends) into the total averages, even if workdays are set in JIRA and Agile to M-F, or any other configuration. There is no way to change the averages to not include those.

It would be very useful for users if they could specify the amount of workdays per week that would go into these averages, especially since many companies using JIRA do not have 7 day work weeks.