I use GIMP for this. Open the PSD in gimp, select the layer with holes (in gimp ALT+click on layer), then select -> remove holes. Then fill the new selection with a color. then select -> inverse, and fill with another color. Then layer -> to image size. Then copy (CTRL+C). then switch back to photoshop, and paste. remove the bg color with the wand. And you ...
(Didn't watch the video)
For Opacity Masks (which is what you've described) to mask everything entirely you need to ensure the black you are using is 100C/100M/100Y/100K or 0R/0G/0B -- all channels need to be solid on the mask. Basically, use the "Registration" swatch.
If you simply use 100% K in areas on the mask, they will be a dark grey and not fully ...
Use Shape's path as mask and subtract it from pre composition
Just deselect everything and then select your precompose layer, take rectangle tool and start drawing shapes in your case (If shapes are complex path then just copy path and paste that as mask)
Now go to layer's mask properties and change it's blending from add to subtract (you can select invert ...
Quick and dirty:
animate your 3 layers, than pre-compose them together;
use this composition as your mask.
This way you can add more layers / shapes later, change the animation, etc. It gives you more flexibility.