The SCORM player embeds the package within an iframe and keeps the Moodle SCORM API in the same window so that the communication all happens within the same window. We have done this since Moodle 2.2 as IE 7 had some strange issues when trying to communicate across multiple windows.
This occasionally causes layout issues with some SCORM packages and it might be a good idea to offer another option and allow the package to open in a window by itself and communicate via js with the parent window that initiated the pop-up.
Jamie Smith wrote an initial patch to do this when trying to workaround an issue with Articulate here:
Articulate have released a patch to their product to allow published scorms to display nicely within an iframe but I think it could be useful to add this option in future anyway.