I was colonising a planet with the Active Core trait and got the Thunderstorms event. I chose the Malevolent option (+50% research, -20% Approval), and then took a look at the tooltips.
The Approval penalty is applied correctly.
The Research bonus, however, is a bit off. 
Two entries for Thunderstorms (and only at +25%, instead of +50%), but no entry for the -25% Active Core research penalty? Well, if you add the bonus and the penalty together, you get +25%. So that would make sense.
And as for the Active Core manufacturing bonus...
...it's called Thunderstorms too.