My questions are:

- to simulate thunderstorm I understand I have to enable "Thunderstorm" under "Simulation" on ALL Illumination channels ( 1 to 4 ). Is it correct ??

You don't have to, but the Simu-L as effect Lamp is not that bright that you see the thunderstorm if the tubes are at 100 %. For this reason there is a field to choose called the "darkening". This will be the effect what we need to darken the main tubes during the thunderstorm. It simulates the dark clouds came up in case of a thunderstorm. So enable "thunderstorm" to all illumination channels and play with the darkening if you get the effect you want to have.

- With that settings, will I get 'flashings' in the ProfiLuxSimu-L and dimming of light intensity on ALL channels (1 to 4) ?? ( or will the 'flashing signals' interfere with the dimmable ballast on channels 1/2 and cause some strange behavior?? )

The flashings will not cause any strange behaviors on your tubes. The only thing you will the at your tubes will be the darkening i talked above.