The one possible area of "collection control" this plugin may now offer is that unlike Book Sync with this plugin you have the ability to add a tag/custom column value when you put a book in a list. I don't know this area of the Kindle Collections plugin very well as I don't use it, but I know meme's plugin allows you to create collections based on a custom column. So in theory you could tie the two together, by configuring a value to put in a column based on the Reading List you added it to and then have that list effectively become a collection on your Kindle. You would not want to automatically clear such a list though or your collection wouldnt last very long
Or so the theory goes - my own usage of Kindle Collections is extremely basic. I create automated collections based on author sort and that is all I want/need.