fundamental problem working with alpha channel in photoshop and after effects

Maybe this will be easier if you turn on the Alpha Chanel in the Comp panel so you are only looking at the alpha channel. Start by adding a blue shape layer to the timeline. Next, try creating two shape layers using rectangles in the same shape layer. Fill one with white and the other with black. Just for fun fil a third with 50% Gray. Put a big gray stroke around the rectangles and maybe even a blue one. You get something like this:

set the view options to Alpha in the comp panel so you can see what is going on with the alpha channel.

Then set the shape layer as a track matte and look at just the alpha channel.

Everything that is white is going to show be opaque, everything that is black will be transparent. If you were to turn on the shape layer and solo it you would see the same thing. Track matte makes the color values and the alpha channels from the source (top) layer control the opacity of the layer below. Cycle through all of the options to see how the values of the Alpha Channel change for each option:

Then as a final check, turn on all of the channels and enable the transparency grid so you can see the actual transparency. If you are going to work with layers it is very important that you have a clear understanding of how "track mattes," alpha, and color channels work. There is nothing odd or unusual about the behavior and it is common across any app that has the ability to use alpha channels for transparency, even Photoshop. 

Use the "Alpha Iverted Matte", because what you are saying to the layer below is that it use the alpha of the layer above and that the white leave it matte. In this case the layer does not use its own alpha but uses that of the layer above.

Track Matte in After Effects