On your first question, it seems like it might work. The code in your functions.php will execute after Simple Sidebars executes, so the sidebars should exist for you to assign a sidebar to a CPT. Give it a try and see how it works out.
On your second question, Simple Sidebars stores the sidebars it creates as records in the options table. It grabs the sidebars created from these options. If you want a sidebar to appear in the pull down list, you'd be better off to fire the code that Simple Sidebars uses to create a sidebar. You could do something conditionally, like check if a Simple Sidebars function exists or the plugin is activated, and if so, call its functions to create the sidebar. Then, they'd exist in the Simple Sidebar options and would appear in the pull down.
You also might get better visibility to post questions like these in the Plugins forum here.