Aside from the question of "can it", you might want to consider "should it".
Let's assume that the two layers of steel are approximately the same thickness.
If you`re using a self tapping screw through a 1/4" steel plate, the threads will be locked into that plate. As the drill tip exits the steel plate and enters the cold formed truss member, it could push against the chord member, create a small gap before it starts drilling, and then create threads in the truss member. Because each layer of steel is held by the threads, there is no way to close this gap, and no clamping force will be created between the two layers of steel.
I`d suggest predrilling the plate (greater than the thread outer diameter).
I think that the situation is worse if the truss member is thinner than the steel plate. At that point, your screw capacity becomes driven by a failure of the thinner plate. Better to drive it "upside down" in this case - predrilling and driving through the thin steel into the thick steel.