Yes, you will have access to PM and you will be able to purchase more items, e.g. a copy of the game. Just remember that Pledge Manager is going to launch quite soon after the end of the campaign because it’s necessary for us to quickly order the appropriate amount of production on the basis of data from PM.
Standard and Deluxe versions have the same box and its content with all unlocked stretch goals. Deluxe version includes also all listed Add-ons (delivered in a separate box whose content fits in the core box, so you can move it there) at a $2 discount.
All game components marked as LIMITED will be unavailable in the retail version of the game. As for all remaining components, there should be no difference. Remember that retailers can also purchase copies on KS, so they will be exactly the same as yours.