PPro 2 seems to give you the red line in desktop mode even if the frame size and frame rate matches the project settings perfectly. This was not the case in PPro 1.5. If I get any more insight into that problem, I will post it here. Anyway it does not affect the image quality or playback rate.
Also not sure if you know this but the latest version of Raylight allows you to drop MXF files directly into Premiere. There is more info at the dvfilm site, http://dvfilm.com/raylight
Yes, always shoot 1080/24PA becasue the frames can be remove without recompression. This is so important that the 1080/24P 3:2 pulldown feature is deliberately absent from Raylight. On the other hand 3:2 pulldown can be removed from 720p60 no problem and with no recompression.
If you have After Effects it does have a 3:2 pulldown feaure that can be used on raylight AVI's that still have pulldown. The result will be recompressed of course.
It's easy with Raylight. Basically you use RayMaker (part of Raylight) to remove the extra frames making it a native 48 frames/sec AVI (for example). Then bring the clip into Premiere and, if you want slow motion as opposed to posterized time (the "CSI Miami" effect which is also possible if you do nothing further), then use Premiere's Interpret footage feature to set the frame rate of the clip to the same rate as your project (like 23.976 for example). Then it becomes slow motion and there is a 1:1 mapping of frames.
Let me know if you have any further questions.