How to fill to only a portion of a precomped shape layer (used as alpha track Matte) for photo

Maybe the naming is confusing you. I animated a mask on a solid, duplicated the layer, expanded the mask, and added a stroke to the mask. The original layer is not layer 2 and I used that as a track matte for layer 3.

I tried to explain that the original tutorial is a very poor and complicated workflow, but if you want to use the original then you are applying fill to the wrong layer. You have to apply Fill to a layer that is below the layer with the video. The presenter's project uses a solid layer, adds an effect, animates the effect, then makes a copy of the layer without linking any of the animations in the copy to the original layer, rotates the duplicate to create the wipe effect. Then instead of pre-composing both of the layers and using that as a track matte for the original image, he duplicates the original footage and uses each independent layer as a track matte for the original footage further complicating the project and making it more difficult to modify the animation in any way. Then, instead of just duplicating the copy of the track matte and dragging it below the image layer, he pre-composes both pairs again, then duplicates again, then applies the Fill effect to both of the copies of the layers and offsets both layers in time, further complicating the animation and the project.

If you want to keep the original comp structure then start by removing the fill from all layers, turn off all layers, except the bottom layer. Apply Fill to the bottom layer, then turn on the next layer. You should see the image with the fill behind it. Then turn on the third layer and you should see the other half of the image. Apply fill to that layer and then turn on the top layer. You should now see the other half of the image. 

Carefully look at the last part of the tutorial where he is applying the fill. It's around 7 minutes in. Look for the little FX icon to appear on layers 2 and 4. Those are the layers with the fill applied.

I'll throw together a tutorial sometime today that shows how to create this kind of a transition using any shape you want. There will be less than 10 keyframes and only 2 nested comps required to create a fancy track matte for any layer.

I'd give that tutorial a C. The workflow is OK but overly complex and almost adequately explained.

If you apply to fill a layer that has transparency then the fill will not fill in the extra pixels. Applying fill to a copy of the pre-comp should not fill in the alpha channel, you should still see an animated curve, but if the fill is applied to the top layer the photo will be hidden. Fill needs to be applied to the layer below the original image. Start soloing layers and you'll figure it out.

The presenter's workflow is way too complicated. You can achieve the very same effect with 3 layers and no pre-comps. I would have animated a mask or a shape layer to generate the track matte, then duplicated it or tied the properties together and added a stroke to the top copy of the mask (track matte) layer. The comp would look like this and it took me less than 5 minutes to create.