exclude an layer from the adjustment layer

Collected files is no indication of project size, a single image sequence could have 4,000 files. AE is a very poor movie editor but it's great for creating shots. If you are building whole sequences with many shots in a single AE comp then you are not using the software in the way it was designed. I have many projects where there are 200 or more layers in a 10 second shot. I render the shot and then edit the sequence in a NLE... That's how it was designed.

If you jump to another program with the same or greater compositing and motion graphics capabilities you're going to run into the same problem if you try and put an entire movie in a compositing program.

Just a friendly workflow suggestion.

To exclude a layer from an adjustment layer you have to re-order the rendering pipeline. In a node editor you add a node, In AE you Pre-compose. Pre-composing is a tool you should use not avoid. There's nothing wrong with it. It does not effect quality. It's all about layers and render order. In 20 years using AE I've never 'been dying here' because of a pre-comp. It's all about planning your work and understanding the render pipeline.

There are changes planned in the visual display of pre-comps in the timeline but the same thing will still hold true, if you want to change the rendering order you have to change the position of the layer in the render stack. Nodes or pre-comps are a way to get that done.