1. when moto sends out an update, you can still install it without an issue as long as you are on the stock rom, and as long as you havent deleted any essential system files. however, when you update, you will lose root access, so keep that in mind before you decide to do it (though usually someone figures out a root method within a week or so afterwards).
2. again, as long as you dont delete the dock apps off of the phone, there should be no difference. if you end up installing a custom rom, that may not be the case