Great to hear you've sorted the close button. Constructive feedback is always welcome - we couldn't improve without it!
The SCORM player is supposed to use the full height/width of the available browser window when pop-up window is selected - earlier releases of Moodle 2.2 didn't do this and we made various improvement such as MDL-31888 MDL-31749 MDL-31381 and possibly others - what version of Moodle 2 are you using? - is it a later version which includes the fixes for those issues?
I don't think we'll enable any custom css stuff from within the SCORM editing page - this is really what the Moodle Themes are for - if the "base" css isn't generic enough (to use fullscreen, no strange borders etc) - then we need to improve the "base" css to be a lot cleaner
If you are using the latest stable release and you find one of the core themes isn't allowing the SCORM player to use the full window height/width feel free to create a bug in the tracker - make sure you include screenshots/scorm package that allows us to reproduce the issue.