Much of what you are wishing for you can already do with the Quick Layers Palette and Find & Select. I know you have used the program for some time, but as you do not mention these methods, are you not aware of them?
Intheory it might be good to have the option to have the layer settings box able to stay open. But I've found that if you are routinely going into the layer settings box to do as you describe,, you are are not working smart.
The Layer settings box is for creating and/or editing layers and layer combinations.
MacBook Pro Retina, 15-inch Yosemite 2.8 GHz Intel Core i7 16 GB 1600 MHz DDR3
Mac OSX 10.11.1
"Implementing Successful Building Information Modeling"