Hi Mirko ,
You are right , if it says you should do 90-100% of the aerobic threshold , it means you are doing the base training on zone 2 where you build aerobic capacity .
Since you are preparing for ultras , most of your training should be under the anaerobic threshold, you should sustain efforts from longer periods without the presence of acid lactic .
I hope I answered you questions
Cheers ,
Pedro Carvalho