.app extension in Spotlight or Alfred

Once you find the file using Alfred, you can copy its path to the clipboard and paste that path into the Go to Folder tool of open/save dialogs.

Find your file in Alfred, press the right arrow key to view the list of operations for that file, the up arrow key to go to the last option (Copy path to clipboard), and then the enter key to activate that option.
Switch back to the open/save dialog, press cmd-shift-g to open the Go to Folder dialog, paste the path in, and hit enter. The file will be selected and you can hit Enter to open/save.

If you're interested in getting some more flexibility out of Open/Save dialogs, I highly recommend Default Folder X. It's immensely powerful and customizable and could eliminate the need for workarounds like this.
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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