The sync question brings up another.
First, yes it should sync automatically as does Kindle for Android and iBooks on iOS. One reason is the nookcolor screen has dead spots. If a button is in a dead spot then it would be an issue. It probably won't affect stock apps but if the nookcolor is rooted then even the Nook for Android app is hindered by dead spots.
So the second question, does the STR have dead spots on the screen?
Explanation: By dead spot I mean a part of the screen that is unresponsive to touch. A major flaw for a touch screen interface.