Did you do the same test with Gigabit only, to see if it's Thunderbolt only issue ? When testing a new config, it's easy to focus more on things we didn't bench on previous hardware in the same way.
Also, are the 2 machines similar spec wise, different CPU, disk (SSD) speed could explain the difference in the direction.
Maybe if that's container, smart thumbnail previews could be the culprit.
Well according to this Thunderbolt network seems flaky
It's probably time to fill a bug report to Apple