1. Can I put Soontir Fel into the bloodstriped TIE Interceptor from the Imperial Aces pack when it comes out, as he is an Interceptor pilot, or do they count as two different ships?

2. Does the other player roll defense dice when their ships is about to be hit by a secondary weapon such as missiles and torpedoes?

Yes and yes

2. yes but take note that there is no range dice modifiers bonus for secondary weps

1. As far as I'm aware they all just count as Interceptors, So you can use any Interceptor model to represent the ship of any Interceptor Pilot card.