How can I have Spotlight Comments actually get indexed by Spotlight?
The comments should normally show up in Spotlight results after you close an information window in Finder. You can tell Spotlight to reindex directories or files with mdimport, but it should do that automatically most of the time.

The Spotlight comments seem to be stored in both .DS_Store files and extended attributes. But if a file is owned by root, Finder doesn't write the comment to an extended attribute, and it won't be seen by Spotlight either.

If you use xattr to add the comments, they are picked up by Spotlight, but they aren't shown in Finder's information windows.

sudo touch test
sudo xattr -w com.apple.metadata:kMDItemFinderComment somecomment test


If you open Finder as root, they are saved in both extended attributes and .DS_Store files.

sudo /System/Library/CoreServices/Finder.app/Contents/MacOS/Finder