How do DVDs avoid the blockyness that plagues dark scenes in most video files?
A single layer DVD has about 4.5 GB of capacity, a dual layer DVD has about 8.5 GB of capacity. Some of this space is taken up by menus and special features, but that still leaves plenty of room for video with minimal compression.

Take a look at the "blocky" videos - they have probably been re-compressed down to 700MB (so they can fit on a CD-R blank) or 1GB (because people love round numbers). Shrinking the video down requires more aggressive compression settings, which results in lower quality video. Sometimes this lower quality exhibits itself in terms of large blocky dark regions.

The other issue is that the compression algorithms used on DVD video are lossy. When you transcode to a lower bitrate codec, the software uncompresses and then recompresses the video. Since the compression is lossy, the uncompress step recovers imperfect video, and that imperfect video is then compressed. This slightly compounds the quality problems.

If you want to make a perfect copy, just rip out the original video. Don't transcode it to a new format.