The linked articles state the testing was done with the mitigations provided in the latest kernel enabled. It does not say that the microcode updates were applied during the testing.

Also there was significant reduced performance when hyperthreading was disabled as required to fully mitigate the threat of the vulnerabilities. If the microcode update changes the behavoir of hyperthreading in order to fully mitigate the vulnerabilities without having to completely disable it then there is a chance these changes effect the performance benefit of hyperthreading.

Given Intel's anti-benchmark license clause without evidence otherwise I assume it is not just a chance but a strong likelihood that the performance benefits are significantly impacted.