I don't know for sure (as I've never bought any plush from the US Pokémon Center website, only from Japan), but I can think of a few reasons that might be the cause.
The first is safety regulations, as different countries have their own codes and guidelines for salable product, especially when it's aimed towards children. If something in the Japanese product would not pass an American safety regulation, it might be changed. We already know that safety regulations impact other aspects of the world of Pokémon merch, as this is why Europe no longer gets the plastic Pokémon figures in the various TCG boxes. Based on the changes you've noted, I actually think this option is probably correct, as loose dangling pieces might be considered to be a choking hazard or some such.
The other possibility might simply be that the products are produced in different factories and so they may use different materials or change certain aspects specifically for ease or cost.