I don't think it's so much of a matter of a well-qualified MTA employee bringing additional value by pulling huge amounts of overtime each year. It's more the principle. The fact is, the highest paid MTA employee last year made nearly as much in base salary + overtime ($396K total) as did the President of the United States (who is paid $400K annually). Granted, many people in many professions make more than $400K, but a vast majority of those people who do aren't government employees.
The outrage over this report has more to do, I suspect, with people questioning the real long-term value of having so many employees working so many overtime hours. Given the MTA has thousands of employees on its payrolls, the consistent year-over-year increase in overtime would suggest that the MTA and the LIRR are not efficiently using their existing workforce. As there has not been a significant increase in service on the LIRR in recent years, the data would suggest that the MTA and LIRR are inefficiently using their existing workforce.
Finally, as several studies have found that one's productivity drops significantly after more than 50 hours of work in a given week, we further need to question whether all of these overtime hours are actually productive or merely leading to even more overtime as work is not efficiently being completed, thereby requiring additional overtime from other employees.
All in all, it points to very sloppy management by the MTA and LIRR of its existing workforce.