meme, I don't get that behaviour. Are you sure you hadn't added it to the main toolbar in some other way in the past before you did the dont_add_to?
I just now did these steps:
Preferences->Plugins->Uninstall Create Kindle Collections
Without closing dialog, Add new plugin of KindleCollections.
That gave me the dialog in the screenshot attached.
I chose the top option of "The main toolbar when the device is connected".
Clicked OK.
Restarted Calibre.
As you can see from the second screenshot your plugin is not present.
But when I plugin my Kindle, the plugin appears as expected?
Your other question about the icons for the Preferences->Customize the toolbar is something that has been bugging me for a while. I did look at the code once and found the reason why it would not display them - there is nothing we as plugin developers can do, it needs Calibre code changes.