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

The simplest answer, from what I can see, is to make sure that all comments are comma-delimited. So, "google music" becomes "google, music" (without quotes). I have been using this as a "tagging" system for the past few years, and it definitely works just like this. I can't remember where exactly I discovered that commas were necessary, but I had the same problem beforehand, and no problems afterward.
The only other hitch I've hit is that occasionally I'll search for a file or folder that I know I've tagged, and it won't show up. This is because sometimes, for no good reason, these comments will just get wiped. I've never figured out how or why this happens, but it doesn't happen often, and it's never caused any serious problems. Regardless, use commas, and that should solve your problem.