There are about 1001 ways to handle the issue manually (during the last few years I have explained some of them), but the OP is correct: when cue tracks are created from a cue sheet that points to a single disc image file and also the disc image file's file format is set to be imported in the Auto-Import settings, the disc image file is automatically imported.
That isn't a problem to me. I have the disc image files in my library but not in my usual views. It is rather easy to tag and exclude them. Sometimes I need the disc image files when I burn MP3 discs for my car player (it does not support gapless playback so I rather burn the disc image file if the album has seamless track transitions).
The "duplicate tracks" issue with separate track files and cue sheets that point to them has been fixed in the latest MC15 builds.