I would like to know the difference between the two IDE programs, I know there is a difference when trying to update, but I would like to see some sort of comparison if possible. Thank you in advance.
I'd like to know that also. They do specifically state e.g. "(Windows Store 1.6.11.0)" as the version but I don't understand why it would be any different from the standard Windows IDE release.
There is a bug I've seen reported here a couple times that only occurs with the Windows Store version:
http://forum.arduino.cc/index.php?topic=438628