You are correct in both counts regarding the two settings to adjust. You need to add about 20-30 pixels in the "Play in New Window" settings to offset the video player settings. Also very important is if you use the 'embed' option in PowerPress, your embeds need to be 20-30 pixels smaller than the "Play in New Window" settings, or your play in new window settings need to be 20-30 pixels larger then your embeds. This is because browsers by default add between 5-10 pixels of padding around the pages to factor in things like vertical scroll bars and such. Essentially once you get the new window size dialed in, the scroll bars should go away and you should have a nice border around your player.
Glad you like 3.0!