I wonder how much it really matters?

On the secure flight data screen, my name shows up as (not my actual name): Jason Fernandez Jones. On my BPs, often it will print JasonFer Jones. But, because the right names are in the right boxes on the website and it matches my GOES data for GE and my GE card, I've not had any issues with PreCheck.

Perhaps one of the DL board contacts could address this issue for us since it is very evidently a DL issue and the TSA/CBP people will tell you to address it with the airline if it doesn't match your trusted traveler name.