I'm pretty sure I already know the answer to this:

What is the point of Fortifications when Thunderhawks (of which the Chaos player has 8 of them) are able to enter into the majority of battles?

This isn't so much a trick question or a clarification. I guess I'm just totally confused why you would make a rule (-2 to damage) but then let something that's fairly common (thunderhawk) to constantly circumvent said rule.

It makes Rogal Dorn totally useless, at least while defending.

Yes, I suppose it's conceivable that an opponent doesn't have all their Thunderhawks out...but why would they not?

Sarim Rune said:

Because the Imperial player targetted them with his damage assignment and destroyed them ?

Dam said:

Unless Breaching is checked at the start of every iteration, I don't see how that's too relevant. If it's not checked, them having the thunderhawk at the beginning of the round means it's breached for the fight, despite damage inflicted on the thunderhawk. If it is checked, then that would make a huge difference in battles as then yes, it would be the first to be destroyed.

but in a game like this where you don't get many new forces for the Imperial player, every attack against you is costly. Having Fortifications seems important yet casually circumvented.

"A unit of Adeptus Mechanicus in the Forbidden
Fortress fall under attack from Chaos Space Marines in
the Lions Gate spaceport and a Chaos Thunderhawk Flight
to the south. Even though the Forbidden Fortress is not
breached, it is considered to be breached for as long as the
Thunderhawk Flight remains engaged in the battle , because
it is a flying unit." (p. 34)

emphasis mine

Similar deal with regular breaches, the other example on the same page. If you kill the units in the area against which the Breach marker is for, you go back to full fortification.

Well then...that's great! That not only makes logical sense but it also makes the rules more palatable. I'm very glad to see I'm wrong in this case.