The title says it. Setting a shield generators texture to invisible (which makes it so there is no block period) will not stop Wither Skulls from traveling through.

There is my setup. Pretty simple, for the shield template just make a box and put a Wither in it. It'll take damage and start shooting skulls. They should travel all over the place.

Playing version 3.0.6 of FTB SF3.

Can I show your setup? Is the box for the wither big enough? What tier is the shield generator? For the wither you might need higher tier as the amount of power required to hold is bigger

I'm in creative mode so that's no problem. Using Creative Capacitor Bank, Tier 4 Shield Gen. Quick note, the skulls don't travel by the shield if you use any other texture.

EDIT: Finished processing