Don't require track mattes to be above the layer it modifies (and also allow re-use)

I currently am duplicating the layer to be used for the track matte for each layer that needs it. added 20 layers to my current job when one would do.

Precomp will work but it removes the ability to edit and adjust layers and see the results over the background and under this track matte.

Why not have track mattes work like parenting, simply choose the layer for a track matte.
Done.

Make a new effect called "Track Matte" which can be applied to the layer. Or fix "Set Matte" to have that option!

The set matte effect is great yes. And may be for visual help in the timeline a lasso could be nice.
And the node based comping for ae would also be awesome in my opinion.

Or, give the "Set Matte" effect some love. Generally, some filters feel like they were completely abandoned. Example: Ramp.

Agreed. Or they could improve the functionality of the set matte, which is absolutely useless if you ever have to precomp. AE really, really should introduce some kind of node-based workflow option. AE is great (for now!) but working exclusively with layers is so old-fashioned for compositing/animation.

Agreed. AE compositions organization should get closer to nodes / graphs

I would love this feature to work how it does in Photoshop. Can make folders (not pre-comps) - and - apply a mask(s) to that folder/group.

For now, we need to create some sort of Master Control Layer that other layers can reference. Could be done with pre-comps or Pick Whipping the properties of your Master Layer.

i have just completed a project where it would really have helped to be able to let multiple layers refer to the same track matte. OK it's easy enough to duplicate them during the build but if you ever need to come back and re-edit something for a client, or worse still need to give that job to someone else to do, you really need total recall of what you duplicated and where/why in order to be able to do this... I'm only human!

This would be so useful!

It would be cool to use one matte for multiple layers, I'm not fussed whether they have to stay above as I find that easy to locate them.