They are sub-divided into core installations.(which btw are sorted alphabetically) For every core there is a boards.txt file which has all the menu options for every board that is included in that core. You can modify that file by shifting the menu entries for the boards that you use a lot to places that you can more easily find them.
And IDE 2 keeps prompting you to update stuff, but apparently you can turn that off.
I actually have some cores in my sketchbook folder which are manually installed but that is a different matter.
Ideally i would even want just a list of recently selected boards. That would really simplify my workflow.