After Effects is a compositing app, which is best served by layers (or nodes for other apps), not an editor which functions best with tracks. Yes, sometimes it gets annoying when you have a lot of layers or a cascading animations, but that is what pre-comping is for. One thing that allows you to reduce unnecessary pre-comping these days is Master Properties. You can have a single pre-comp and then add multiple parameters to the Essential Graphics panel. Those properties are then exposed in your Master Comp. What's amazing is that you can duplicate this pre-comp as many times as you want and change those Master Properties without affecting the other instances of your comp. This massive feature makes pre-comping less irritating since it can drastically reduce how much you need to do it, but it also lets you build out very powerful custom rigs.
This doesn't directly solve your issue of wanting two layers to occupy the same space on the timeline, but depending on what you're doing it could make your workflow simpler and potentially allow you to have fewer layers overall.
Here's an 11 minute School of Motion tutorial on them: https://www.schoolofmotion.com/tutorials/master-properties-after-effects